ENST00000717943.1:n.289-1840G>A

Variant names:

• chr10-128962085-C-T
• rs10829529
• ENST00000717943.1:n.289-1840G>A

Variant summary

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

The ENST00000717943.1(ENSG00000232985):​n.289-1840G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,254 control chromosomes in the GnomAD database, including 1,333 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 0.12 (1333 hom., cov: 33)
• Consequence: ENSG00000232985 ENST00000717943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 0 publications found

Genes affected

ENSG00000232985 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 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
ENSG00000232985	ENST00000717943.1	n.289-1840G>A		intron_variant	Intron 1 of 3
ENSG00000232985	ENST00000837851.1	n.289-2407G>A		intron_variant	Intron 1 of 2
ENSG00000232985	ENST00000837852.1	n.288-1814G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18078 AN: 152136 Hom.: 1332 Cov.: 33

Gnomad AFR AF: 0.0348

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.119 AC: 18095 AN: 152254 Hom.: 1333 Cov.: 33 AF XY: 0.119 AC XY: 8827 AN XY: 74440

African (AFR) AF: 0.0348 AC: 1446 AN: 41572

American (AMR) AF: 0.139 AC: 2132 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 510 AN: 3470

East Asian (EAS) AF: 0.135 AC: 696 AN: 5148

South Asian (SAS) AF: 0.188 AC: 908 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10610

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10569 AN: 68012

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.120 Hom.: 161

Bravo AF: 0.117

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.47
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10829529; hg19: chr10-130760349; COSMIC: COSV71668545;