rs6426636

chr1-20408972-G-Achr1-20408972-G-T

Variant summary

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

The NR_033887.1(LINC01141):n.212-2703C>T variant causes a intron, non coding transcript 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 NR_033887.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01141	NR_033887.1	n.212-2703C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01141	ENST00000426428.5	n.200-2703C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.654

Alfa AF: 0.633 Hom.: 12380

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6426636; hg19: chr1-20735465;