2-142166583-A-C

Variant names:

• chr2-142166583-A-C
• rs1882164

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 0.54 in 151,820 control chromosomes in the GnomAD database, including 23,381 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 0.54 (23381 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 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: 0.540 AC: 81851 AN: 151702 Hom.: 23329 Cov.: 31

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.540 AC: 81957 AN: 151820 Hom.: 23381 Cov.: 31 AF XY: 0.540 AC XY: 40062 AN XY: 74190

African (AFR) AF: 0.739 AC: 30618 AN: 41426

American (AMR) AF: 0.497 AC: 7573 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 1998 AN: 3462

East Asian (EAS) AF: 0.357 AC: 1844 AN: 5160

South Asian (SAS) AF: 0.594 AC: 2854 AN: 4802

European-Finnish (FIN) AF: 0.463 AC: 4864 AN: 10500

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.449 AC: 30518 AN: 67936

Other (OTH) AF: 0.533 AC: 1122 AN: 2106

Alfa AF: 0.483 Hom.: 9388

Bravo AF: 0.548

Asia WGS AF: 0.551 AC: 1909 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.34
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1882164; hg19: chr2-142924152;