2-4916875-C-T

Variant names:

• chr2-4916875-C-T
• rs721087

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 0.495 in 151,696 control chromosomes in the GnomAD database, including 19,359 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 0.50 (19359 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 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: 0.495 AC: 75043 AN: 151578 Hom.: 19339 Cov.: 30

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.495 AC: 75109 AN: 151696 Hom.: 19359 Cov.: 30 AF XY: 0.496 AC XY: 36769 AN XY: 74102

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.494

Alfa AF: 0.453 Hom.: 32650

Bravo AF: 0.513

Asia WGS AF: 0.634 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs721087; hg19: chr2-4964465;