chr1-157501265-C-T

Variant names:

• chr1-157501265-C-T
• rs2317057

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 0.211 in 151,932 control chromosomes in the GnomAD database, including 4,123 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 0.21 (4123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.113
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 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: 0.211 AC: 32046 AN: 151814 Hom.: 4126 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.211 AC: 32038 AN: 151932 Hom.: 4123 Cov.: 32 AF XY: 0.220 AC XY: 16321 AN XY: 74238

African (AFR) AF: 0.0824 AC: 3415 AN: 41438

American (AMR) AF: 0.248 AC: 3793 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2350 AN: 5168

South Asian (SAS) AF: 0.348 AC: 1677 AN: 4816

European-Finnish (FIN) AF: 0.360 AC: 3786 AN: 10520

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15805 AN: 67926

Other (OTH) AF: 0.197 AC: 417 AN: 2112

Alfa AF: 0.157 Hom.: 456

Bravo AF: 0.196

Asia WGS AF: 0.358 AC: 1242 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.4
DANN	Benign	0.56
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2317057; hg19: chr1-157471055;