rs2943636

Variant names:

• chr2-226222568-G-A
• rs2943636

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 0.451 in 152,044 control chromosomes in the GnomAD database, including 15,721 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 0.45 (15721 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.509 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: 0.451 AC: 68475 AN: 151926 Hom.: 15705 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.451 AC: 68521 AN: 152044 Hom.: 15721 Cov.: 32 AF XY: 0.447 AC XY: 33236 AN XY: 74330

African (AFR) AF: 0.360 AC: 14949 AN: 41484

American (AMR) AF: 0.518 AC: 7915 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1987 AN: 3472

East Asian (EAS) AF: 0.476 AC: 2460 AN: 5164

South Asian (SAS) AF: 0.518 AC: 2500 AN: 4824

European-Finnish (FIN) AF: 0.399 AC: 4206 AN: 10550

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32986 AN: 67962

Other (OTH) AF: 0.482 AC: 1020 AN: 2114

Alfa AF: 0.477 Hom.: 3397

Bravo AF: 0.455

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.63
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2943636; hg19: chr2-227087284;