rs893769

chr2-119082508-A-Cchr2-119082508-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.454

Alfa AF: 0.487 Hom.: 37491

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

Splicing

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

Publications

LitVar

Other links and lift over

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