rs3917647

Variant names:

• chr1-169632102-G-A
• rs3917647

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 0.523 in 151,820 control chromosomes in the GnomAD database, including 21,488 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 0.52 (21488 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79281 AN: 151702 Hom.: 21452 Cov.: 30

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.523 AC: 79369 AN: 151820 Hom.: 21488 Cov.: 30 AF XY: 0.517 AC XY: 38354 AN XY: 74210

African (AFR) AF: 0.645 AC: 26665 AN: 41366

American (AMR) AF: 0.438 AC: 6680 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3464

East Asian (EAS) AF: 0.271 AC: 1398 AN: 5162

South Asian (SAS) AF: 0.383 AC: 1837 AN: 4796

European-Finnish (FIN) AF: 0.460 AC: 4854 AN: 10544

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34350 AN: 67926

Other (OTH) AF: 0.518 AC: 1090 AN: 2106

Alfa AF: 0.512 Hom.: 2756

Bravo AF: 0.527

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.32
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3917647; hg19: chr1-169601340;