rs960792

chr2-203884527-T-C

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 0.405 in 152,074 control chromosomes in the GnomAD database, including 13,477 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 0.40 (13477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

ACMG classification

Verdict is Benign. Variant got -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 = 0.655 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: 0.405 AC: 61588 AN: 151958 Hom.: 13484 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.405 AC: 61580 AN: 152074 Hom.: 13477 Cov.: 32 AF XY: 0.403 AC XY: 29966 AN XY: 74334

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.466

Alfa AF: 0.460 Hom.: 4943

Bravo AF: 0.400

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs960792; hg19: chr2-204749250;