rs1125798

Variant names:

• chr10-108058538-C-T
• rs1125798
• ENST00000425050.5:n.113+10644G>A

Variant summary

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

The ENST00000425050.5(LINC01435):​n.113+10644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,806 control chromosomes in the GnomAD database, including 16,085 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 0.43 (16085 hom., cov: 32)
• Consequence: LINC01435 ENST00000425050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01435	NR_125760.1	n.112+10644G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000425050.5	n.113+10644G>A		intron_variant	Intron 1 of 4	3
LINC01435	ENST00000595603.6	n.328+308G>A		intron_variant	Intron 3 of 6	5
LINC01435	ENST00000600953.3	n.348+308G>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65124 AN: 151688 Hom.: 16036 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.430 AC: 65219 AN: 151806 Hom.: 16085 Cov.: 32 AF XY: 0.424 AC XY: 31428 AN XY: 74166

African (AFR) AF: 0.686 AC: 28429 AN: 41418

American (AMR) AF: 0.381 AC: 5801 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1379 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1052 AN: 5142

South Asian (SAS) AF: 0.313 AC: 1505 AN: 4810

European-Finnish (FIN) AF: 0.247 AC: 2599 AN: 10512

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23249 AN: 67898

Other (OTH) AF: 0.395 AC: 833 AN: 2108

Alfa AF: 0.374 Hom.: 9062

Bravo AF: 0.448

Asia WGS AF: 0.284 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs1125798; hg19: chr10-109818296;