rs10513523

Variant names:

• chr3-157894433-C-T
• rs10513523
• ENST00000651134.1:n.781+1287G>A

Variant summary

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

The ENST00000651134.1(ENSG00000242536):​n.781+1287G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 152,070 control chromosomes in the GnomAD database, including 162 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 0.019 (162 hom., cov: 32)
• Consequence: ENSG00000242536 ENST00000651134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

Genes affected

ENSG00000242536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000242536	ENST00000651134.1	n.781+1287G>A		intron_variant	Intron 6 of 12

Frequencies

GnomAD3 genomes AF: 0.0192 AC: 2923 AN: 151952 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.00530

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00656

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0193 AC: 2940 AN: 152070 Hom.: 162 Cov.: 32 AF XY: 0.0216 AC XY: 1606 AN XY: 74338

African (AFR) AF: 0.00540 AC: 224 AN: 41476

American (AMR) AF: 0.0908 AC: 1386 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3472

East Asian (EAS) AF: 0.135 AC: 697 AN: 5168

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4818

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10566

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00656 AC: 446 AN: 67994

Other (OTH) AF: 0.0194 AC: 41 AN: 2110

Alfa AF: 0.0205 Hom.: 30

Bravo AF: 0.0254

Asia WGS AF: 0.0620 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.17
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10513523; hg19: chr3-157612222;