rs893769

Variant names:

• chr2-119082508-A-C
• rs893769

Your query was ambiguous. Multiple possible variants found:

• chr2-119082508-A-C
• chr2-119082508-A-T

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 0.422 in 152,040 control chromosomes in the GnomAD database, including 14,516 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 0.42 (14516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 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: 0.422 AC: 64138 AN: 151922 Hom.: 14510 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.422 AC: 64173 AN: 152040 Hom.: 14516 Cov.: 32 AF XY: 0.424 AC XY: 31544 AN XY: 74316

African (AFR) AF: 0.257 AC: 10644 AN: 41492

American (AMR) AF: 0.450 AC: 6872 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5170

South Asian (SAS) AF: 0.481 AC: 2311 AN: 4802

European-Finnish (FIN) AF: 0.524 AC: 5525 AN: 10548

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34022 AN: 67964

Other (OTH) AF: 0.454 AC: 957 AN: 2110

Alfa AF: 0.475 Hom.: 75641

Bravo AF: 0.410

Asia WGS AF: 0.387 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.76
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs893769; hg19: chr2-119840084; COSMIC: COSV60101336;