2-233775246-C-T

Variant names:

• chr2-233775246-C-T
• rs4663972

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 0.752 in 152,098 control chromosomes in the GnomAD database, including 43,400 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 0.75 (43400 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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: 0.752 AC: 114308 AN: 151980 Hom.: 43381 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.752 AC: 114374 AN: 152098 Hom.: 43400 Cov.: 32 AF XY: 0.759 AC XY: 56406 AN XY: 74354

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.733

Alfa AF: 0.760 Hom.: 40731

Bravo AF: 0.735

Asia WGS AF: 0.821 AC: 2854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.96
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663972; hg19: chr2-234683892;