chr2-233302326-G-A

Variant names:

• chr2-233302326-G-A
• rs6759896

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 0.461 in 151,976 control chromosomes in the GnomAD database, including 17,446 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 (17446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 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: 0.461 AC: 70041 AN: 151862 Hom.: 17430 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.461 AC: 70083 AN: 151976 Hom.: 17446 Cov.: 32 AF XY: 0.461 AC XY: 34255 AN XY: 74282

African (AFR) AF: 0.269 AC: 11143 AN: 41438

American (AMR) AF: 0.417 AC: 6362 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1812 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2176 AN: 5172

South Asian (SAS) AF: 0.629 AC: 3027 AN: 4814

European-Finnish (FIN) AF: 0.510 AC: 5365 AN: 10520

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38669 AN: 67984

Other (OTH) AF: 0.457 AC: 964 AN: 2110

Alfa AF: 0.522 Hom.: 24587

Bravo AF: 0.442

Asia WGS AF: 0.447 AC: 1551 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6759896; hg19: chr2-234210972; COSMIC: COSV69623490;