rs3917651

Variant names:

• chr1-169630824-C-T
• rs3917651

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0537 in 152,294 control chromosomes in the GnomAD database, including 251 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 0.054 (251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0916 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: 0.0538 AC: 8191 AN: 152176 Hom.: 250 Cov.: 32

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.00827

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0537 AC: 8185 AN: 152294 Hom.: 251 Cov.: 32 AF XY: 0.0535 AC XY: 3982 AN XY: 74454

African (AFR) AF: 0.0494 AC: 2052 AN: 41558

American (AMR) AF: 0.0448 AC: 686 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3472

East Asian (EAS) AF: 0.00829 AC: 43 AN: 5190

South Asian (SAS) AF: 0.0989 AC: 477 AN: 4822

European-Finnish (FIN) AF: 0.0700 AC: 742 AN: 10606

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3844 AN: 68030

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0549 Hom.: 495

Bravo AF: 0.0499

Asia WGS AF: 0.0480 AC: 167 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	0.91
DANN	Benign	0.74
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs3917651; hg19: chr1-169600062;