rs13238709

Positions:

• chr7-101140455-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 0.432 in 151,742 control chromosomes in the GnomAD database, including 14,418 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 0.43 (14418 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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: 0.432 AC: 65456 AN: 151624 Hom.: 14415 Cov.: 30

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.432 AC: 65477 AN: 151742 Hom.: 14418 Cov.: 30 AF XY: 0.427 AC XY: 31658 AN XY: 74164

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.395

Alfa AF: 0.426 Hom.: 14472

Bravo AF: 0.428

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13238709; hg19: chr7-100783736;