3-1596929-A-G

Variant names:

• chr3-1596929-A-G
• rs6779648

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.509 in 151,566 control chromosomes in the GnomAD database, including 21,131 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 0.51 (21131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.675 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: 0.509 AC: 77139 AN: 151446 Hom.: 21130 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.509 AC: 77164 AN: 151566 Hom.: 21131 Cov.: 32 AF XY: 0.511 AC XY: 37821 AN XY: 74030

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.528

Alfa AF: 0.590 Hom.: 33558

Bravo AF: 0.493

Asia WGS AF: 0.573 AC: 1988 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	19
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6779648; hg19: chr3-1638613;