10-129252913-C-T

Variant names:

• chr10-129252913-C-T
• rs541392
• ENST00000685862.2:n.181-15959G>A

Variant summary

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

The ENST00000685862.2(ENSG00000289087):​n.181-15959G>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 ENST00000685862.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 publications found

Genes affected

ENSG00000289087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000685862.2	n.181-15959G>A		intron_variant	Intron 1 of 1
ENSG00000289087	ENST00000686818.1	n.180-15983G>A		intron_variant	Intron 1 of 1
ENSG00000289087	ENST00000828092.1	n.180-9930G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.569 AC: 23555 AN: 41426

American (AMR) AF: 0.824 AC: 12602 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.664 AC: 2303 AN: 3466

East Asian (EAS) AF: 0.973 AC: 5026 AN: 5166

South Asian (SAS) AF: 0.757 AC: 3639 AN: 4810

European-Finnish (FIN) AF: 0.826 AC: 8757 AN: 10596

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51535 AN: 67984

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs541392; hg19: chr10-131051177;