rs13105878

Variant names:

• chr4-110796991-C-A
• rs13105878
• ENST00000512794.1:n.203C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01438	ENST00000512794.1	n.203C>A		non_coding_transcript_exon_variant	Exon 2 of 2	4
LINC01438	ENST00000754041.1	n.440C>A		non_coding_transcript_exon_variant	Exon 3 of 3

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.125 AC: 1 AN: 8

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0296732), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.0162 AC: 674 AN: 41544

American (AMR) AF: 0.0546 AC: 834 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0675 AC: 234 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.0651 AC: 314 AN: 4822

European-Finnish (FIN) AF: 0.0933 AC: 986 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6470 AN: 68008

Other (OTH) AF: 0.0721 AC: 152 AN: 2108

Alfa AF: 0.0831 Hom.: 1165

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
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs13105878; hg19: chr4-111718147;