rs10862167

Variant names:

• chr12-76566967-A-C
• rs10862167
• ENST00000551082.2:n.66-3744A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

ENSG00000257526 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000551082.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105369850	NR_188080.1		n.397-3744A>C		intron	N/A
	LOC105369850	NR_188081.1		n.397-3744A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257526	ENST00000551082.2	TSL:3	n.66-3744A>C		intron	N/A
	ENSG00000257526	ENST00000702157.2		n.440-3744A>C		intron	N/A
	ENSG00000257526	ENST00000832799.1		n.418+4609A>C		intron	N/A

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

African (AFR) AF: 0.756 AC: 31355 AN: 41466

American (AMR) AF: 0.861 AC: 13150 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3005 AN: 3472

East Asian (EAS) AF: 0.643 AC: 3330 AN: 5180

South Asian (SAS) AF: 0.787 AC: 3792 AN: 4818

European-Finnish (FIN) AF: 0.820 AC: 8654 AN: 10558

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59139 AN: 68000

Other (OTH) AF: 0.836 AC: 1766 AN: 2112

Alfa AF: 0.857 Hom.: 40357

Bravo AF: 0.826

Asia WGS AF: 0.697 AC: 2426 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.8
DANN	Benign	0.47
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10862167; hg19: chr12-76960747;