12-20015153-T-C

Variant names:

• chr12-20015153-T-C
• rs10505843
• ENST00000716354.1:n.4510+125T>C

Variant summary

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

The ENST00000716354.1(ENSG00000255910):​n.4510+125T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,944 control chromosomes in the GnomAD database, including 33,163 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 0.64 (33158 hom., cov: 31)
  • Exomes 𝑓: 1.0 (5 hom.)
• Consequence: ENSG00000255910 ENST00000716354.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 3 publications found

Genes affected

ENSG00000255910 (HGNC:):

LINC02398 (HGNC:53325): (long intergenic non-protein coding RNA 2398)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02398	NR_040098.1	n.344+125T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255910	ENST00000716354.1	n.4510+125T>C		intron_variant	Intron 6 of 10
ENSG00000255910	ENST00000716355.1	n.5496+125T>C		intron_variant	Intron 6 of 12
ENSG00000255910	ENST00000716356.1	n.5842+125T>C		intron_variant	Intron 5 of 11

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96619 AN: 151816 Hom.: 33146 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 1.00 AC: 10 AN: 10 Hom.: 5 AF XY: 1.00 AC XY: 10 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 10 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.636 AC: 96657 AN: 151934 Hom.: 33158 Cov.: 31 AF XY: 0.639 AC XY: 47420 AN XY: 74252

African (AFR) AF: 0.374 AC: 15488 AN: 41378

American (AMR) AF: 0.664 AC: 10141 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2528 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2291 AN: 5146

South Asian (SAS) AF: 0.638 AC: 3072 AN: 4812

European-Finnish (FIN) AF: 0.837 AC: 8844 AN: 10572

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52037 AN: 67976

Other (OTH) AF: 0.624 AC: 1316 AN: 2110

Alfa AF: 0.626 Hom.: 2476

Bravo AF: 0.615

Asia WGS AF: 0.562 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs10505843; hg19: chr12-20168087;