rs10013495

Variant names:

• chr4-144584486-C-T
• rs10013495
• ENST00000649263.1:n.328-168508G>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-168508G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,130 control chromosomes in the GnomAD database, including 5,001 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 0.23 (5001 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340
• Publications: 6 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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
ENSG00000285713	ENST00000649263.1	n.328-168508G>A		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-168508G>A		intron_variant	Intron 2 of 14

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35656 AN: 152012 Hom.: 4995 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.235 AC: 35702 AN: 152130 Hom.: 5001 Cov.: 32 AF XY: 0.236 AC XY: 17547 AN XY: 74372

African (AFR) AF: 0.358 AC: 14866 AN: 41500

American (AMR) AF: 0.299 AC: 4562 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 646 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1704 AN: 5160

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1110 AN: 10604

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.156 AC: 10588 AN: 67988

Other (OTH) AF: 0.237 AC: 501 AN: 2110

Alfa AF: 0.199 Hom.: 1374

Bravo AF: 0.252

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.1
DANN	Benign	0.84
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10013495; hg19: chr4-145505638;