rs946261

Variant names:

• chr1-203188745-C-T
• rs946261

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 0.477 in 152,054 control chromosomes in the GnomAD database, including 19,959 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 0.48 (19959 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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: 0.477 AC: 72525 AN: 151936 Hom.: 19967 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.477 AC: 72514 AN: 152054 Hom.: 19959 Cov.: 32 AF XY: 0.476 AC XY: 35397 AN XY: 74328

African (AFR) AF: 0.202 AC: 8379 AN: 41472

American (AMR) AF: 0.401 AC: 6129 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1833 AN: 5166

South Asian (SAS) AF: 0.570 AC: 2748 AN: 4824

European-Finnish (FIN) AF: 0.644 AC: 6803 AN: 10570

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42576 AN: 67964

Other (OTH) AF: 0.480 AC: 1012 AN: 2110

Alfa AF: 0.577 Hom.: 115979

Bravo AF: 0.441

Asia WGS AF: 0.426 AC: 1484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.62
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs946261; hg19: chr1-203157873;