rs13241797

Positions:

• chr7-63199262-C-T

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 0.218 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.228

Alfa AF: 0.244 Hom.: 806

Bravo AF: 0.214

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13241797; hg19: chr7-62659640;