rs12113526

chr7-41873169-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;