dbSNP rs61757218: DNAH8:p.Thr3924Met (chr6-38938181-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_001206927.2(DNAH8):c.11771C>T(p.Thr3924Met) variant causes a missense change. The variant allele was found at a frequency of 0.00617 in 1,613,926 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0066 ( 7 hom., cov: 31)

Exomes 𝑓: 0.0061 ( 31 hom. )

Consequence

DNAH8
NM_001206927.2 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:1B:5

Conservation

PhyloP100: 6.16

Publications

10 publications found

Variant links:

Genes affected

DNAH8 (HGNC:2952): (dynein axonemal heavy chain 8) The protein encoded by this gene is a heavy chain of an axonemal dynein involved in sperm and respiratory cilia motility. Axonemal dyneins generate force through hydrolysis of ATP and binding to microtubules. [provided by RefSeq, Jan 2012]

DNAH8 links:

DNAH8-AS1 (HGNC:40188): (DNAH8 antisense RNA 1)

DNAH8-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.014879525).

BP6

Variant 6-38938181-C-T is Benign according to our data. Variant chr6-38938181-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 402771.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00663 (1009/152274) while in subpopulation AFR AF = 0.00917 (381/41552). AF 95% confidence interval is 0.00841. There are 7 homozygotes in GnomAd4. There are 486 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001206927.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DNAH8	NM_001206927.2	MANE Select	c.11771C>T	p.Thr3924Met	missense	Exon 78 of 93	NP_001193856.1	A0A075B6F3
DNAH8	NM_001371.4		c.11120C>T	p.Thr3707Met	missense	Exon 77 of 92	NP_001362.2	Q96JB1-1
DNAH8-AS1	NR_038401.1		n.61-1789G>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DNAH8	ENST00000327475.11	TSL:5 MANE Select	c.11771C>T	p.Thr3924Met	missense	Exon 78 of 93	ENSP00000333363.7	A0A075B6F3
DNAH8	ENST00000359357.7	TSL:2	c.11120C>T	p.Thr3707Met	missense	Exon 76 of 91	ENSP00000352312.3	Q96JB1-1
DNAH8	ENST00000449981.6	TSL:5	c.11771C>T	p.Thr3924Met	missense	Exon 77 of 82	ENSP00000415331.2	H0Y7V4

Frequencies

GnomAD3 genomes

AF:

0.00663

AC:

1009

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00922

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00832

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00125

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00661

Gnomad OTH

AF:

0.00573

GnomAD2 exomes

AF:

0.00518

AC:

1298

AN:

250738

AF XY:

0.00504

show subpopulations

Gnomad AFR exome

AF:

0.00855

Gnomad AMR exome

AF:

0.00535

Gnomad ASJ exome

AF:

0.00367

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00159

Gnomad NFE exome

AF:

0.00705

Gnomad OTH exome

AF:

0.00555

GnomAD4 exome

AF:

0.00613

AC:

8956

AN:

1461652

Hom.:

Cov.:

AF XY:

0.00599

AC XY:

4352

AN XY:

727130

show subpopulations

African (AFR)

AF:

0.00998

AC:

334

AN:

33478

American (AMR)

AF:

0.00523

AC:

234

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.00432

AC:

113

AN:

26136

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39696

South Asian (SAS)

AF:

0.00204

AC:

176

AN:

86258

European-Finnish (FIN)

AF:

0.00184

AC:

AN:

53238

Middle Eastern (MID)

AF:

0.00468

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00681

AC:

7572

AN:

1111962

Other (OTH)

AF:

0.00664

AC:

401

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

472

944

1417

1889

2361

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

286

572

858

1144

1430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00663

AC:

1009

AN:

152274

Hom.:

Cov.:

AF XY:

0.00653

AC XY:

486

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.00917

AC:

381

AN:

41552

American (AMR)

AF:

0.00831

AC:

127

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00490

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.00145

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00122

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00661

AC:

450

AN:

68028

Other (OTH)

AF:

0.00567

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

105

157

210

262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00629

Hom.:

Bravo

AF:

0.00707

TwinsUK

AF:

0.00917

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.0113

AC:

ESP6500EA

AF:

0.00663

AC:

ExAC

AF:

0.00510

AC:

619

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00676

EpiControl

AF:

0.00699

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (4)

not specified (1)

Primary ciliary dyskinesia (1)

Spermatogenic failure 46 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.14

Eigen

Pathogenic

0.99

Eigen_PC

Pathogenic

0.91

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

0.97

MetaRNN

Benign

0.015

MetaSVM

Uncertain

0.075

MutationAssessor

Pathogenic

4.1

PhyloP100

6.2

PrimateAI

Uncertain

0.62

PROVEAN

Pathogenic

-5.9

REVEL

Uncertain

0.37

Sift

Pathogenic

0.0

Polyphen

1.0

Vest4

0.79

MVP

0.87

MPC

0.58

ClinPred

0.084

GERP RS

5.6

Varity_R

0.64

gMVP

0.68

Mutation Taster

=91/9

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over