rs10862167

Positions:

• chr12-76566967-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000551082.2(ENSG00000257526):​n.66-3744A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,092 control chromosomes in the GnomAD database, including 51,884 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 0.82 (51884 hom., cov: 32)
• Consequence: ENSG00000257526 ENST00000551082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369850	NR_188080.1	n.397-3744A>C		intron_variant
LOC105369850	NR_188081.1	n.397-3744A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257526	ENST00000551082.2	n.66-3744A>C		intron_variant		3
ENSG00000257526	ENST00000702157.1	n.429-3744A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125217 AN: 151972 Hom.: 51862 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.824 AC: 125288 AN: 152092 Hom.: 51884 Cov.: 32 AF XY: 0.820 AC XY: 60981 AN XY: 74322

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.836

Alfa AF: 0.858 Hom.: 29834

Bravo AF: 0.826

Asia WGS AF: 0.697 AC: 2426 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10862167; hg19: chr12-76960747;