rs13230029

chr7-142759369-G-Cchr7-142759369-G-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 0.538 in 144,584 control chromosomes in the GnomAD database, including 17,934 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 0.54 (17934 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.538 AC: 77752 AN: 144474 Hom.: 17931 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.461

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.538 AC: 77809 AN: 144584 Hom.: 17934 Cov.: 33 AF XY: 0.534 AC XY: 37832 AN XY: 70820

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.540

Alfa AF: 0.529 Hom.: 1418

Asia WGS AF: 0.273 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.57
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13230029; hg19: chr7-142467216;