rs12113526

Variant names:

• chr7-41873169-G-A
• rs12113526
• ENST00000839902.1:n.566+1048G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000839902.1(ENSG00000309263):​n.566+1048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000309263 ENST00000839902.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 0 publications found

Genes affected

ENSG00000309263 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000309263	ENST00000839902.1	n.566+1048G>A		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.826 AC: 34290 AN: 41538

American (AMR) AF: 0.588 AC: 8989 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3470

East Asian (EAS) AF: 0.355 AC: 1835 AN: 5172

South Asian (SAS) AF: 0.665 AC: 3206 AN: 4820

European-Finnish (FIN) AF: 0.706 AC: 7465 AN: 10568

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.660 AC: 44879 AN: 67966

Other (OTH) AF: 0.687 AC: 1450 AN: 2112

Alfa AF: 0.695 Hom.: 4830

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
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs12113526; hg19: chr7-41912767;