ENST00000493899.2:n.542-34989A>G

Variant names:

• chr10-62850958-T-C
• rs1509957
• ENST00000493899.2:n.542-34989A>G

Variant summary

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

The ENST00000493899.2(ENSG00000289487):​n.542-34989A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 152,038 control chromosomes in the GnomAD database, including 17,497 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 (17497 hom., cov: 32)
• Consequence: ENSG00000289487 ENST00000493899.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 14 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=-0.89).
• 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.542-34989A>G		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72536 AN: 151920 Hom.: 17485 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.493

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: 0.477 AC: 72595 AN: 152038 Hom.: 17497 Cov.: 32 AF XY: 0.481 AC XY: 35758 AN XY: 74344

African (AFR) AF: 0.428 AC: 17739 AN: 41456

American (AMR) AF: 0.420 AC: 6411 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1642 AN: 3472

East Asian (EAS) AF: 0.390 AC: 2013 AN: 5156

South Asian (SAS) AF: 0.492 AC: 2376 AN: 4828

European-Finnish (FIN) AF: 0.532 AC: 5621 AN: 10572

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

European-Non Finnish (NFE) AF: 0.518 AC: 35180 AN: 67956

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.502 Hom.: 73797

Bravo AF: 0.463

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.41
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs1509957; hg19: chr10-64610718;