rs6732653

Variant names:

• chr2-60636698-G-A
• rs6732653

Your query was ambiguous. Multiple possible variants found:

• chr2-60636698-G-A
• chr2-60636698-G-C
• chr2-60636698-G-T

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 0.355 in 151,982 control chromosomes in the GnomAD database, including 10,464 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 0.35 (10464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.51 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: 0.355 AC: 53855 AN: 151864 Hom.: 10436 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.355 AC: 53930 AN: 151982 Hom.: 10464 Cov.: 32 AF XY: 0.348 AC XY: 25858 AN XY: 74284

African (AFR) AF: 0.516 AC: 21362 AN: 41436

American (AMR) AF: 0.328 AC: 5005 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3468

East Asian (EAS) AF: 0.109 AC: 566 AN: 5170

South Asian (SAS) AF: 0.195 AC: 941 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3117 AN: 10546

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20944 AN: 67958

Other (OTH) AF: 0.325 AC: 686 AN: 2112

Alfa AF: 0.322 Hom.: 23947

Bravo AF: 0.366

Asia WGS AF: 0.166 AC: 577 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.46
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs6732653; hg19: chr2-60863833;