rs10496515

Variant names:

• chr2-116313637-T-C
• rs10496515
• ENST00000847484.1:n.295+18198T>C

Variant summary

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

The ENST00000847484.1(ENSG00000310137):​n.295+18198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0931 in 151,704 control chromosomes in the GnomAD database, including 711 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 0.093 (711 hom., cov: 32)
• Consequence: ENSG00000310137 ENST00000847484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 2 publications found

Genes affected

ENSG00000310137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847484.1. 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
	ENSG00000310137	ENST00000847484.1		n.295+18198T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14115 AN: 151584 Hom.: 709 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0728

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.0561

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.0931 AC: 14126 AN: 151704 Hom.: 711 Cov.: 32 AF XY: 0.0931 AC XY: 6907 AN XY: 74176

African (AFR) AF: 0.0957 AC: 3973 AN: 41494

American (AMR) AF: 0.106 AC: 1603 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0728 AC: 252 AN: 3462

East Asian (EAS) AF: 0.109 AC: 565 AN: 5172

South Asian (SAS) AF: 0.152 AC: 732 AN: 4820

European-Finnish (FIN) AF: 0.0561 AC: 595 AN: 10606

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0912 AC: 6170 AN: 67642

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0934 Hom.: 358

Bravo AF: 0.0962

Asia WGS AF: 0.146 AC: 506 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0090
DANN	Benign	0.36
PhyloP100		-2.7

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: rs10496515;

hg19: chr2-117071213;