1-157501265-C-T

Variant names:

• chr1-157501265-C-T
• rs2317057

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 0.211 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0824

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.197

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2317057; hg19: chr1-157471055;