2-646674-T-C

Variant names:

• chr2-646674-T-C
• rs10190052

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.782 AC: 32414 AN: 41434

American (AMR) AF: 0.859 AC: 13128 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2549 AN: 3470

East Asian (EAS) AF: 0.917 AC: 4741 AN: 5168

South Asian (SAS) AF: 0.859 AC: 4141 AN: 4820

European-Finnish (FIN) AF: 0.849 AC: 8959 AN: 10554

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56289 AN: 68000

Other (OTH) AF: 0.827 AC: 1745 AN: 2110

Alfa AF: 0.820 Hom.: 32998

Bravo AF: 0.819

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.026
DANN	Benign	0.30
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10190052; hg19: chr2-646674;