rs1125798

chr10-108058538-C-T

Variant summary

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

The NR_125760.1(LINC01435):n.112+10644G>A variant causes a intron, non coding transcript 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 NR_125760.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01435	NR_125760.1	n.112+10644G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01435	ENST00000425050.5	n.113+10644G>A		intron_variant, non_coding_transcript_variant		3
LINC01435	ENST00000595603.5	n.328+308G>A		intron_variant, non_coding_transcript_variant		5
LINC01435	ENST00000600953.3	n.348+308G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.395

Alfa AF: 0.373 Hom.: 7636

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1125798; hg19: chr10-109818296;