rs3917647

Positions:

• chr1-169632102-G-A

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 0.523 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

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 (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.518

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3917647; hg19: chr1-169601340;