rs12113526

Variant names:

• chr7-41873169-G-A
• rs12113526

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 0.692 in 152,138 control chromosomes in the GnomAD database, including 37,372 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 0.69 (37372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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: 0.691 AC: 105097 AN: 152020 Hom.: 37314 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.692 AC: 105211 AN: 152138 Hom.: 37372 Cov.: 32 AF XY: 0.688 AC XY: 51170 AN XY: 74356

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.687

Alfa AF: 0.690 Hom.: 4578

Bravo AF: 0.684

Asia WGS AF: 0.588 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12113526; hg19: chr7-41912767;