rs3000811

Positions:

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

Variant summary

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

The ENST00000445817.1(LINC01641):​n.210+5141G>A 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 0.812 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01641	XR_001737828.1	n.213+5141G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01641	ENST00000445817.1	n.210+5141G>A		intron_variant, non_coding_transcript_variant		1
LINC01641	ENST00000660249.1	n.247+5141G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.805

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3000811; hg19: chr1-227588456;