rs7761629

Variant names:

• chr6-38725585-G-A
• rs7761629
• NM_001206927.2:c.525+2114G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-38725585-G-A
• chr6-38725585-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001206927.2(DNAH8):​c.525+2114G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0512 in 152,108 control chromosomes in the GnomAD database, including 226 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 0.051 (226 hom., cov: 31)
• Consequence: DNAH8 NM_001206927.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0512 (7789/152108) while in subpopulation EAS AF= 0.0525 (272/5182). AF 95% confidence interval is 0.0494. There are 226 homozygotes in gnomad4. There are 3936 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 226 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH8	NM_001206927.2	c.525+2114G>A		intron_variant	Intron 3 of 92	ENST00000327475.11	NP_001193856.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH8	ENST00000327475.11	c.525+2114G>A		intron_variant	Intron 3 of 92	5	NM_001206927.2	ENSP00000333363.7
DNAH8	ENST00000373278.8	c.525+2114G>A		intron_variant	Intron 3 of 4	1		ENSP00000362375.4
DNAH8	ENST00000359357.7	c.-42+2114G>A		intron_variant	Intron 2 of 90	2		ENSP00000352312.3
DNAH8	ENST00000449981.6	c.525+2114G>A		intron_variant	Intron 2 of 81	5		ENSP00000415331.2

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7793 AN: 151990 Hom.: 226 Cov.: 31

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.0600

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

GnomAD4 genome AF: 0.0512 AC: 7789 AN: 152108 Hom.: 226 Cov.: 31 AF XY: 0.0529 AC XY: 3936 AN XY: 74356

Gnomad4 AFR AF: 0.0512

Gnomad4 AMR AF: 0.0477

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0525

Gnomad4 SAS AF: 0.0492

Gnomad4 FIN AF: 0.0807

Gnomad4 NFE AF: 0.0469

Gnomad4 OTH AF: 0.0594

Alfa AF: 0.0464 Hom.: 207

Bravo AF: 0.0488

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.74

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

LitVar

Other links and lift over

dbSNP: rs7761629; hg19: chr6-38693361;