rs914947

Variant names:

• chr1-242686516-T-C
• rs914947

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 0.73 in 152,126 control chromosomes in the GnomAD database, including 40,701 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 0.73 (40701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.730 AC: 110983 AN: 152008 Hom.: 40690 Cov.: 32

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.730 AC: 111036 AN: 152126 Hom.: 40701 Cov.: 32 AF XY: 0.727 AC XY: 54103 AN XY: 74376

African (AFR) AF: 0.714 AC: 29646 AN: 41510

American (AMR) AF: 0.640 AC: 9770 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2655 AN: 3468

East Asian (EAS) AF: 0.813 AC: 4209 AN: 5176

South Asian (SAS) AF: 0.747 AC: 3594 AN: 4812

European-Finnish (FIN) AF: 0.702 AC: 7418 AN: 10566

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51155 AN: 67998

Other (OTH) AF: 0.746 AC: 1576 AN: 2114

Alfa AF: 0.719 Hom.: 6349

Bravo AF: 0.724

Asia WGS AF: 0.734 AC: 2554 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.67
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs914947; hg19: chr1-242849818;