chr2-646674-T-C

Position:

• chr2-646674-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 0.822 in 152,044 control chromosomes in the GnomAD database, including 51,472 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 0.82 (51472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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: 0.822 AC: 124841 AN: 151926 Hom.: 51447 Cov.: 32

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.917

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.822 AC: 124923 AN: 152044 Hom.: 51472 Cov.: 32 AF XY: 0.825 AC XY: 61356 AN XY: 74336

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.859

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.827

Alfa AF: 0.829 Hom.: 10125

Bravo AF: 0.819

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.026
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10190052; hg19: chr2-646674;