2-635721-T-C

Variant names:

• chr2-635721-T-C
• rs6755502

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 0.852 in 152,188 control chromosomes in the GnomAD database, including 55,381 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 0.85 (55381 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.852 AC: 129607 AN: 152068 Hom.: 55337 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.850

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.852 AC: 129709 AN: 152188 Hom.: 55381 Cov.: 32 AF XY: 0.855 AC XY: 63580 AN XY: 74388

African (AFR) AF: 0.887 AC: 36839 AN: 41516

American (AMR) AF: 0.870 AC: 13318 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4748 AN: 5164

South Asian (SAS) AF: 0.860 AC: 4151 AN: 4826

European-Finnish (FIN) AF: 0.849 AC: 8981 AN: 10576

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.828 AC: 56346 AN: 68016

Other (OTH) AF: 0.844 AC: 1783 AN: 2112

Alfa AF: 0.851 Hom.: 22816

Bravo AF: 0.854

Asia WGS AF: 0.893 AC: 3100 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.6
DANN	Benign	0.64
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs6755502; hg19: chr2-635721;