2-156321104-G-C

Variant names:

• chr2-156321104-G-C
• rs1150143

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 0.559 in 152,048 control chromosomes in the GnomAD database, including 25,706 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 0.56 (25706 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85033 AN: 151930 Hom.: 25702 Cov.: 33

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.559 AC: 85048 AN: 152048 Hom.: 25706 Cov.: 33 AF XY: 0.561 AC XY: 41697 AN XY: 74310

African (AFR) AF: 0.331 AC: 13722 AN: 41434

American (AMR) AF: 0.497 AC: 7595 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2439 AN: 3472

East Asian (EAS) AF: 0.439 AC: 2268 AN: 5168

South Asian (SAS) AF: 0.603 AC: 2906 AN: 4816

European-Finnish (FIN) AF: 0.716 AC: 7565 AN: 10560

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.684 AC: 46518 AN: 67990

Other (OTH) AF: 0.592 AC: 1252 AN: 2116

Alfa AF: 0.610 Hom.: 3578

Bravo AF: 0.525

Asia WGS AF: 0.553 AC: 1925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1150143; hg19: chr2-157177616;