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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01435	ENST00000809134.1		n.158+566G>A		intron	N/A
	LINC01435	ENST00000809136.1		n.540+20814G>A		intron	N/A
	LINC01435	ENST00000809137.1		n.541-7674G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2419006;

hg19: chr10-110188914;