chr2-226190165-A-C

Variant names:

• chr2-226190165-A-C
• rs2943633

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 0.456 in 151,984 control chromosomes in the GnomAD database, including 16,383 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 0.46 (16383 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 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: 0.456 AC: 69198 AN: 151866 Hom.: 16367 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.456 AC: 69230 AN: 151984 Hom.: 16383 Cov.: 32 AF XY: 0.450 AC XY: 33465 AN XY: 74286

African (AFR) AF: 0.325 AC: 13480 AN: 41452

American (AMR) AF: 0.452 AC: 6894 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2343 AN: 5134

South Asian (SAS) AF: 0.547 AC: 2635 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4327 AN: 10582

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35788 AN: 67962

Other (OTH) AF: 0.488 AC: 1032 AN: 2114

Alfa AF: 0.507 Hom.: 84204

Bravo AF: 0.449

Asia WGS AF: 0.569 AC: 1981 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.063
DANN	Benign	0.58
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs2943633; hg19: chr2-227054881;