rs13241797

Variant names:

• chr7-63199262-C-T
• rs13241797

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 0.218 in 152,124 control chromosomes in the GnomAD database, including 4,295 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 0.22 (4295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 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: 0.218 AC: 33147 AN: 152006 Hom.: 4295 Cov.: 32

Gnomad AFR AF: 0.0610

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.218 AC: 33151 AN: 152124 Hom.: 4295 Cov.: 32 AF XY: 0.223 AC XY: 16564 AN XY: 74354

African (AFR) AF: 0.0608 AC: 2525 AN: 41540

American (AMR) AF: 0.322 AC: 4913 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3464

East Asian (EAS) AF: 0.151 AC: 782 AN: 5170

South Asian (SAS) AF: 0.289 AC: 1390 AN: 4810

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18796 AN: 67986

Other (OTH) AF: 0.228 AC: 482 AN: 2110

Alfa AF: 0.241 Hom.: 1606

Bravo AF: 0.214

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.89
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs13241797; hg19: chr7-62659640;