rs13105878

chr4-110796991-C-A

Variant summary

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

The ENST00000512794.1(LINC01438):n.203C>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 0.0648 in 152,168 control chromosomes in the GnomAD database, including 488 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 0.065 (488 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: LINC01438 ENST00000512794.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0932 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.203C>A		non_coding_transcript_exon_variant	2/2	4

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9864 AN: 152038 Hom.: 488 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0675

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0933

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.0724

GnomAD4 exome AF: 0.167 AC: 2 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 2 AN XY: 12

Gnomad4 ASJ exome AF: 0.500

Gnomad4 NFE exome AF: 0.125

GnomAD4 genome AF: 0.0648 AC: 9859 AN: 152156 Hom.: 488 Cov.: 32 AF XY: 0.0628 AC XY: 4672 AN XY: 74354

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0675

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0651

Gnomad4 FIN AF: 0.0933

Gnomad4 NFE AF: 0.0951

Gnomad4 OTH AF: 0.0721

Alfa AF: 0.0909 Hom.: 890

Bravo AF: 0.0609

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13105878; hg19: chr4-111718147;