rs6843082

chr4-110796911-G-Achr4-110796911-G-T

Variant summary

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

The ENST00000512794.1(LINC01438):n.123G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 151,970 control chromosomes in the GnomAD database, including 38,234 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 0.70 (38230 hom., cov: 32)
  • Exomes 𝑓: 1.0 (4 hom.)
• Consequence: LINC01438 ENST00000512794.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

Genes affected

LINC01438 (HGNC:50757): (long intergenic non-protein coding RNA 1438)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01438	ENST00000512794.1	n.123G>A		non_coding_transcript_exon_variant	2/2	4

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106427 AN: 151846 Hom.: 38204 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.263

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.705

GnomAD4 exome AF: 1.00 AC: 8 AN: 8 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 6 AN XY: 6

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.701 AC: 106499 AN: 151962 Hom.: 38230 Cov.: 32 AF XY: 0.685 AC XY: 50881 AN XY: 74290

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.703

Alfa AF: 0.746 Hom.: 64244

Bravo AF: 0.696

Asia WGS AF: 0.497 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	11
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6843082; hg19: chr4-111718067;