10-108429156-C-T

Variant names:

• chr10-108429156-C-T
• rs2419006
• ENST00000809134.1:n.158+566G>A

Variant summary

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

The ENST00000809134.1(LINC01435):​n.158+566G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,120 control chromosomes in the GnomAD database, including 53,727 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 0.84 (53727 hom., cov: 31)
• Consequence: LINC01435 ENST00000809134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 2 publications found

Genes affected

LINC01435 (HGNC:50753): (long intergenic non-protein coding RNA 1435)

LOC105378477 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378477	XR_946308.2	n.911+20814G>A		intron_variant	Intron 3 of 4
LOC105378477	XR_946309.2	n.634+20814G>A		intron_variant	Intron 3 of 4
LOC105378477	XR_946310.2	n.613+20814G>A		intron_variant	Intron 3 of 4
LOC105378477	XR_946312.2	n.912-7674G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000809134.1	n.158+566G>A		intron_variant	Intron 1 of 3
LINC01435	ENST00000809136.1	n.540+20814G>A		intron_variant	Intron 3 of 4
LINC01435	ENST00000809137.1	n.541-7674G>A		intron_variant	Intron 3 of 3
LINC01435	ENST00000809138.1	n.144+566G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127561 AN: 152002 Hom.: 53679 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.839 AC: 127667 AN: 152120 Hom.: 53727 Cov.: 31 AF XY: 0.840 AC XY: 62470 AN XY: 74352

African (AFR) AF: 0.792 AC: 32856 AN: 41480

American (AMR) AF: 0.885 AC: 13523 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5144 AN: 5150

South Asian (SAS) AF: 0.869 AC: 4192 AN: 4826

European-Finnish (FIN) AF: 0.835 AC: 8824 AN: 10572

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57467 AN: 68016

Other (OTH) AF: 0.843 AC: 1781 AN: 2112

Alfa AF: 0.844 Hom.: 106511

Bravo AF: 0.843

Asia WGS AF: 0.941 AC: 3272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.44
DANN	Benign	0.48
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2419006; hg19: chr10-110188914;