10-62852129-A-G

Variant names:

• chr10-62852129-A-G
• rs10509173
• ENST00000493899.2:n.542-36160T>C

Variant summary

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

The ENST00000493899.2(ENSG00000289487):​n.542-36160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,832 control chromosomes in the GnomAD database, including 17,476 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 0.48 (17476 hom., cov: 30)
• Consequence: ENSG00000289487 ENST00000493899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 3 publications found

Genes affected

ENSG00000289487 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 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
ENSG00000289487	ENST00000493899.2	n.542-36160T>C		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72458 AN: 151716 Hom.: 17464 Cov.: 30

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.478 AC: 72516 AN: 151832 Hom.: 17476 Cov.: 30 AF XY: 0.481 AC XY: 35706 AN XY: 74210

African (AFR) AF: 0.428 AC: 17703 AN: 41376

American (AMR) AF: 0.420 AC: 6410 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1642 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2023 AN: 5166

South Asian (SAS) AF: 0.492 AC: 2363 AN: 4804

European-Finnish (FIN) AF: 0.531 AC: 5591 AN: 10528

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35177 AN: 67914

Other (OTH) AF: 0.477 AC: 1000 AN: 2098

Alfa AF: 0.512 Hom.: 10259

Bravo AF: 0.463

Asia WGS AF: 0.469 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.39
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs10509173; hg19: chr10-64611889;