rs10492051

Variant names:

• chr12-121087863-G-A
• rs10492051
• ENST00000837362.1:n.478C>T

Variant summary

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

The ENST00000837362.1(ENSG00000308932):​n.478C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,206 control chromosomes in the GnomAD database, including 619 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 0.070 (619 hom., cov: 32)
• Consequence: ENSG00000308932 ENST00000837362.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 6 publications found

Genes affected

ENSG00000308932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837362.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308932	ENST00000837362.1		n.478C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000308932	ENST00000837363.1		n.982C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000308932	ENST00000837364.1		n.427C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10678 AN: 152088 Hom.: 621 Cov.: 32

Gnomad AFR AF: 0.0155

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0421

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.0653

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

GnomAD4 genome AF: 0.0702 AC: 10682 AN: 152206 Hom.: 619 Cov.: 32 AF XY: 0.0722 AC XY: 5371 AN XY: 74410

African (AFR) AF: 0.0155 AC: 643 AN: 41536

American (AMR) AF: 0.0421 AC: 643 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 291 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0924 AC: 446 AN: 4826

European-Finnish (FIN) AF: 0.185 AC: 1955 AN: 10588

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0963 AC: 6550 AN: 68002

Other (OTH) AF: 0.0641 AC: 135 AN: 2106

Alfa AF: 0.0910 Hom.: 388

Bravo AF: 0.0551

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.1
DANN	Benign	0.45
PhyloP100		-0.0090

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10492051;

hg19: chr12-121525666;