rs3000811

Variant names:

• chr1-227400755-G-A
• rs3000811
• ENST00000445817.1:n.210+5141G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-227400755-G-A
• chr1-227400755-G-C

Variant summary

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

The ENST00000445817.1(LINC01641):​n.210+5141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 151,886 control chromosomes in the GnomAD database, including 50,108 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 0.81 (50108 hom., cov: 29)
• Consequence: LINC01641 ENST00000445817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 6 publications found

Genes affected

LINC01641 (HGNC:52428): (long intergenic non-protein coding RNA 1641)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01641	NR_187381.1	n.247+5141G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01641	ENST00000445817.1	n.210+5141G>A		intron_variant	Intron 2 of 3	1
LINC01641	ENST00000660249.1	n.247+5141G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123204 AN: 151768 Hom.: 50063 Cov.: 29

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.812 AC: 123308 AN: 151886 Hom.: 50108 Cov.: 29 AF XY: 0.810 AC XY: 60145 AN XY: 74242

African (AFR) AF: 0.760 AC: 31458 AN: 41376

American (AMR) AF: 0.764 AC: 11658 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3470

East Asian (EAS) AF: 0.795 AC: 4090 AN: 5146

South Asian (SAS) AF: 0.801 AC: 3849 AN: 4808

European-Finnish (FIN) AF: 0.845 AC: 8909 AN: 10548

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57816 AN: 67980

Other (OTH) AF: 0.805 AC: 1689 AN: 2098

Alfa AF: 0.815 Hom.: 8166

Bravo AF: 0.806

Asia WGS AF: 0.772 AC: 2686 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	0.60
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs3000811; hg19: chr1-227588456;