rs7629386

Variant names:

• chr3-40925416-C-T
• rs7629386

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.294 in 152,072 control chromosomes in the GnomAD database, including 6,898 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 0.29 (6898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44710 AN: 151954 Hom.: 6890 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.294 AC: 44739 AN: 152072 Hom.: 6898 Cov.: 32 AF XY: 0.288 AC XY: 21381 AN XY: 74334

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.0585

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.291

Alfa AF: 0.316 Hom.: 13481

Bravo AF: 0.286

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.63
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7629386; hg19: chr3-40966907;