Genetic Variant DNAAF11:n.667C>T (chr8-132702241-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007060728.1(DNAAF11):n.667C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,070 control chromosomes in the GnomAD database, including 3,302 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 3302 hom., cov: 32)

Exomes 𝑓: 0.14 ( 0 hom. )

Consequence

DNAAF11
XR_007060728.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.813

Publications

6 publications found

Variant links:

Genes affected

DNAAF11 (HGNC:16725): (dynein axonemal assembly factor 11) The protein encoded by this gene contains several leucine-rich repeat domains and appears to be involved in the motility of cilia. Defects in this gene are a cause of primary ciliary dyskinesia-19 (CILD19). Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 11 and 22. [provided by RefSeq, Apr 2016]

DNAAF11 links:

TMEM71 (HGNC:26572): (transmembrane protein 71) Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

TMEM71 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
DNAAF11	XR_007060728.1 link	n.667C>T	non_coding_transcript_exon_variant	Exon 1 of 13
DNAAF11	XM_006716538.4 link	c.-426C>T	5_prime_UTR_variant	Exon 1 of 14	XP_006716601.2
DNAAF11	XM_011516950.3 link	c.-426C>T	5_prime_UTR_variant	Exon 1 of 13	XP_011515252.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM71	ENST00000522780.5 link	c.264-14586C>T		intron_variant	Intron 2 of 3	4		ENSP00000428772.1		H0YB65
TMEM71	ENST00000524079.5 link	n.-2C>T		upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27795

AN:

151930

Hom.:

3303

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0450

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.307

Gnomad FIN

AF:

0.242

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.212

Gnomad OTH

AF:

0.203

GnomAD4 exome

AF:

0.136

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.143

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.183

AC:

27793

AN:

152048

Hom.:

3302

Cov.:

AF XY:

0.189

AC XY:

14078

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.0448

AC:

1862

AN:

41518

American (AMR)

AF:

0.298

AC:

4556

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

630

AN:

3470

East Asian (EAS)

AF:

0.314

AC:

1621

AN:

5162

South Asian (SAS)

AF:

0.308

AC:

1483

AN:

4812

European-Finnish (FIN)

AF:

0.242

AC:

2549

AN:

10532

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.212

AC:

14419

AN:

67970

Other (OTH)

AF:

0.200

AC:

421

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1097

2194

3291

4388

5485

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.207

Hom.:

5778

Bravo

AF:

0.178

Asia WGS

AF:

0.290

AC:

1008

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.43

(source)

DANN

Benign

0.64

PhyloP100

-0.81

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over