ENST00000493899.2:n.542-36385T>A

Variant names:

• chr10-62852354-A-T
• rs10761670
• ENST00000493899.2:n.542-36385T>A

Variant summary

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

The ENST00000493899.2(ENSG00000289487):​n.542-36385T>A 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 151,894 control chromosomes in the GnomAD database, including 17,500 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 (17500 hom., cov: 31)
• Consequence: ENSG00000289487 ENST00000493899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.564
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 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.542-36385T>A		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72516 AN: 151776 Hom.: 17488 Cov.: 31

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: 0.491

Gnomad FIN AF: 0.532

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: 72575 AN: 151894 Hom.: 17500 Cov.: 31 AF XY: 0.481 AC XY: 35729 AN XY: 74236

African (AFR) AF: 0.428 AC: 17738 AN: 41420

American (AMR) AF: 0.420 AC: 6403 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2022 AN: 5168

South Asian (SAS) AF: 0.491 AC: 2360 AN: 4810

European-Finnish (FIN) AF: 0.532 AC: 5595 AN: 10520

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

European-Non Finnish (NFE) AF: 0.518 AC: 35208 AN: 67946

Other (OTH) AF: 0.477 AC: 1002 AN: 2102

Alfa AF: 0.388 Hom.: 1112

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	-0.80
CADD	Benign	7.0
DANN	Benign	0.82
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10761670; hg19: chr10-64612114;