rs13238709

Variant names:

• chr7-101140455-C-T
• rs13238709

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 0.432 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.466 AC: 19275 AN: 41358

American (AMR) AF: 0.316 AC: 4814 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2440 AN: 5132

South Asian (SAS) AF: 0.419 AC: 2007 AN: 4788

European-Finnish (FIN) AF: 0.421 AC: 4439 AN: 10546

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29444 AN: 67918

Other (OTH) AF: 0.395 AC: 833 AN: 2108

Alfa AF: 0.428 Hom.: 21141

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
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs13238709; hg19: chr7-100783736;