rs10507342

Variant names:

• chr13-25045592-T-C
• rs10507342
• ENST00000762481.1:n.666+94A>G

Variant summary

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

The ENST00000762481.1(ENSG00000299308):​n.666+94A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 152,324 control chromosomes in the GnomAD database, including 195 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 0.021 (195 hom., cov: 33)
• Consequence: ENSG00000299308 ENST00000762481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 2 publications found

Genes affected

ENSG00000299308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370119	XR_001749796.2	n.1788+94A>G		intron_variant	Intron 1 of 2
LOC105370119	XR_941760.4	n.1853+94A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299308	ENST00000762481.1	n.666+94A>G		intron_variant	Intron 3 of 4
ENSG00000299308	ENST00000762482.1	n.1841+94A>G		intron_variant	Intron 2 of 3
ENSG00000299308	ENST00000762483.1	n.267+94A>G		intron_variant	Intron 2 of 3
ENSG00000299308	ENST00000762484.1	n.274+94A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3269 AN: 152206 Hom.: 195 Cov.: 33

Gnomad AFR AF: 0.00485

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0215 AC: 3268 AN: 152324 Hom.: 195 Cov.: 33 AF XY: 0.0247 AC XY: 1836 AN XY: 74472

African (AFR) AF: 0.00483 AC: 201 AN: 41590

American (AMR) AF: 0.0261 AC: 399 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1259 AN: 5182

South Asian (SAS) AF: 0.0561 AC: 271 AN: 4828

European-Finnish (FIN) AF: 0.0362 AC: 384 AN: 10610

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 686 AN: 68026

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.0130 Hom.: 5

Bravo AF: 0.0210

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.3
DANN	Benign	0.90
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs10507342; hg19: chr13-25619730;