1-155159197-A-G

Variant names:

• chr1-155159197-A-G
• rs4276913

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 0.393 in 152,086 control chromosomes in the GnomAD database, including 12,870 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 0.39 (12870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 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: 0.393 AC: 59763 AN: 151968 Hom.: 12874 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.393 AC: 59770 AN: 152086 Hom.: 12870 Cov.: 32 AF XY: 0.400 AC XY: 29741 AN XY: 74308

African (AFR) AF: 0.254 AC: 10533 AN: 41510

American (AMR) AF: 0.516 AC: 7874 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1258 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4230 AN: 5172

South Asian (SAS) AF: 0.479 AC: 2310 AN: 4824

European-Finnish (FIN) AF: 0.465 AC: 4920 AN: 10572

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27352 AN: 67966

Other (OTH) AF: 0.385 AC: 812 AN: 2108

Alfa AF: 0.401 Hom.: 16103

Bravo AF: 0.396

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.76
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs4276913; hg19: chr1-155131673;