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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378258	XR_007063492.1	n.5133C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105378258	XR_945451.4	n.5133C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308932	ENST00000837362.1	n.478C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000308932	ENST00000837363.1	n.982C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308932	ENST00000837364.1	n.427C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308947	ENST00000837477.1	n.540+448G>A		intron_variant	Intron 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 v4.3

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

Other links and lift over

dbSNP: rs10492051; hg19: chr12-121525666;