1-20409376-C-T

Variant names:

• chr1-20409376-C-T
• rs7514144
• ENST00000426428.5:n.200-3107G>A

Variant summary

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

The ENST00000426428.5(LINC01141):​n.200-3107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,134 control chromosomes in the GnomAD database, including 50,807 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 0.82 (50807 hom., cov: 32)
• Consequence: LINC01141 ENST00000426428.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.45
• Publications: 3 publications found

Genes affected

LINC01141 (HGNC:49455): (long intergenic non-protein coding RNA 1141)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01141	NR_033887.1	n.212-3107G>A		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01141	ENST00000426428.5	n.200-3107G>A		intron_variant	Intron 1 of 11	1
LINC01141	ENST00000418743.6	n.620-3107G>A		intron_variant	Intron 1 of 4	3
LINC01141	ENST00000423486.1	n.59-3107G>A		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124086 AN: 152016 Hom.: 50760 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.839

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.816 AC: 124190 AN: 152134 Hom.: 50807 Cov.: 32 AF XY: 0.815 AC XY: 60632 AN XY: 74378

African (AFR) AF: 0.840 AC: 34867 AN: 41522

American (AMR) AF: 0.829 AC: 12670 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3074 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3961 AN: 5164

South Asian (SAS) AF: 0.749 AC: 3605 AN: 4810

European-Finnish (FIN) AF: 0.782 AC: 8273 AN: 10580

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54924 AN: 67994

Other (OTH) AF: 0.842 AC: 1775 AN: 2108

Alfa AF: 0.808 Hom.: 25090

Bravo AF: 0.823

Asia WGS AF: 0.780 AC: 2714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.75
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs7514144; hg19: chr1-20735869;