10-129252913-C-T

Variant names:

• chr10-129252913-C-T
• rs541392
• ENST00000685862.1:n.180-15959G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000685862.1(ENSG00000289087):​n.180-15959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,054 control chromosomes in the GnomAD database, including 40,595 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 0.72 (40595 hom., cov: 31)
• Consequence: ENSG00000289087 ENST00000685862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

ENSG00000289087 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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
ENSG00000289087	ENST00000685862.1	n.180-15959G>A		intron_variant	Intron 1 of 1
ENSG00000289087	ENST00000686818.1	n.180-15983G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109798 AN: 151936 Hom.: 40572 Cov.: 31

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.973

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.722 AC: 109852 AN: 152054 Hom.: 40595 Cov.: 31 AF XY: 0.730 AC XY: 54223 AN XY: 74328

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.973

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.826

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.730

Alfa AF: 0.741 Hom.: 7135

Bravo AF: 0.719

Asia WGS AF: 0.830 AC: 2888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs541392; hg19: chr10-131051177;