6-38789602-C-T

Variant names:

• chr6-38789602-C-T
• rs7756191
• NM_001206927.2:c.2584-201C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001206927.2(DNAH8):​c.2584-201C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,926 control chromosomes in the GnomAD database, including 8,857 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.33 (8857 hom., cov: 32)
• Consequence: DNAH8 NM_001206927.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.182
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• spermatogenic failure 46

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
• spermatogenic failure 5

  Inheritance: AR Classification: MODERATE Submitted by: Franklin by Genoox
• primary ciliary dyskinesia

  Inheritance: AR Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 6-38789602-C-T is Benign according to our data. Variant chr6-38789602-C-T is described in ClinVar as Benign. ClinVar VariationId is 1236141.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH8	NM_001206927.2	c.2584-201C>T		intron_variant	Intron 18 of 92	ENST00000327475.11	NP_001193856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH8	ENST00000327475.11	c.2584-201C>T		intron_variant	Intron 18 of 92	5	NM_001206927.2	ENSP00000333363.7
DNAH8	ENST00000359357.7	c.1933-201C>T		intron_variant	Intron 16 of 90	2		ENSP00000352312.3
DNAH8	ENST00000449981.6	c.2584-201C>T		intron_variant	Intron 17 of 81	5		ENSP00000415331.2

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50738 AN: 151808 Hom.: 8858 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.352

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.334 AC: 50752 AN: 151926 Hom.: 8857 Cov.: 32 AF XY: 0.334 AC XY: 24828 AN XY: 74246

African (AFR) AF: 0.260 AC: 10764 AN: 41432

American (AMR) AF: 0.313 AC: 4773 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1518 AN: 3468

East Asian (EAS) AF: 0.391 AC: 2015 AN: 5158

South Asian (SAS) AF: 0.405 AC: 1952 AN: 4814

European-Finnish (FIN) AF: 0.326 AC: 3441 AN: 10548

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25091 AN: 67920

Other (OTH) AF: 0.351 AC: 741 AN: 2112

Alfa AF: 0.361 Hom.: 28174

Bravo AF: 0.331

Asia WGS AF: 0.359 AC: 1251 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7756191; hg19: chr6-38757378; COSMIC: COSV59482837;