rs12534413

chr7-131769205-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 0.143 in 152,216 control chromosomes in the GnomAD database, including 1,629 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 0.14 (1629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 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: 0.143 AC: 21747 AN: 152098 Hom.: 1630 Cov.: 33

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0890

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.143 AC: 21761 AN: 152216 Hom.: 1629 Cov.: 33 AF XY: 0.144 AC XY: 10684 AN XY: 74424

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0890

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.124

Alfa AF: 0.139 Hom.: 691

Bravo AF: 0.135

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	7.0
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12534413; hg19: chr7-131453964;