rs6426636

Variant names:

• chr1-20408972-G-A
• rs6426636
• ENST00000426428.5:n.200-2703C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-20408972-G-A
• chr1-20408972-G-T

Variant summary

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

The ENST00000426428.5(LINC01141):​n.200-2703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,580 control chromosomes in the GnomAD database, including 29,705 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 0.62 (29705 hom., cov: 32)
• Consequence: LINC01141 ENST00000426428.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01141	NR_033887.1	n.212-2703C>T		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01141	ENST00000426428.5	n.200-2703C>T		intron_variant	Intron 1 of 11	1
LINC01141	ENST00000418743.6	n.620-2703C>T		intron_variant	Intron 1 of 4	3
LINC01141	ENST00000423486.1	n.59-2703C>T		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94254 AN: 151464 Hom.: 29671 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.622 AC: 94337 AN: 151580 Hom.: 29705 Cov.: 32 AF XY: 0.623 AC XY: 46175 AN XY: 74074

African (AFR) AF: 0.517 AC: 21345 AN: 41298

American (AMR) AF: 0.706 AC: 10760 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2540 AN: 3462

East Asian (EAS) AF: 0.750 AC: 3851 AN: 5136

South Asian (SAS) AF: 0.661 AC: 3190 AN: 4826

European-Finnish (FIN) AF: 0.609 AC: 6402 AN: 10510

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44026 AN: 67792

Other (OTH) AF: 0.654 AC: 1377 AN: 2106

Alfa AF: 0.634 Hom.: 14150

Bravo AF: 0.626

Asia WGS AF: 0.704 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.15
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6426636; hg19: chr1-20735465;