chr1-157705207-G-T

Variant names:

• chr1-157705207-G-T
• rs2317230

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 0.552 in 152,084 control chromosomes in the GnomAD database, including 26,198 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 0.55 (26198 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 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: 0.551 AC: 83788 AN: 151966 Hom.: 26139 Cov.: 32

Gnomad AFR AF: 0.872

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.552 AC: 83898 AN: 152084 Hom.: 26198 Cov.: 32 AF XY: 0.547 AC XY: 40661 AN XY: 74352

African (AFR) AF: 0.872 AC: 36198 AN: 41510

American (AMR) AF: 0.489 AC: 7471 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2111 AN: 5174

South Asian (SAS) AF: 0.423 AC: 2040 AN: 4820

European-Finnish (FIN) AF: 0.412 AC: 4359 AN: 10568

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28719 AN: 67940

Other (OTH) AF: 0.520 AC: 1101 AN: 2116

Alfa AF: 0.484 Hom.: 2519

Bravo AF: 0.571

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.35
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2317230; hg19: chr1-157674997;