1-43937817-G-T

Variant names:

• chr1-43937817-G-T
• rs6671164
• ENST00000657883.1:n.*101C>A

Variant summary

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

The ENST00000657883.1(LINC02918):​n.*101C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,074 control chromosomes in the GnomAD database, including 31,750 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 0.60 (31750 hom., cov: 31)
• Consequence: LINC02918 ENST00000657883.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 7 publications found

Genes affected

LINC02918 (HGNC:55649): (long intergenic non-protein coding RNA 2918)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02918	XR_947283.2	n.*79C>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02918	ENST00000657883.1	n.*101C>A		downstream_gene_variant
LINC02918	ENST00000784651.1	n.*79C>A		downstream_gene_variant
LINC02918	ENST00000784652.1	n.*79C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91108 AN: 151956 Hom.: 31747 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.785

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.599 AC: 91131 AN: 152074 Hom.: 31750 Cov.: 31 AF XY: 0.597 AC XY: 44352 AN XY: 74348

African (AFR) AF: 0.229 AC: 9476 AN: 41464

American (AMR) AF: 0.631 AC: 9641 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2369 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3176 AN: 5158

South Asian (SAS) AF: 0.608 AC: 2923 AN: 4808

European-Finnish (FIN) AF: 0.742 AC: 7852 AN: 10578

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.785 AC: 53391 AN: 68000

Other (OTH) AF: 0.640 AC: 1348 AN: 2106

Alfa AF: 0.583 Hom.: 2165

Bravo AF: 0.577

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.9
DANN	Benign	0.84
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6671164; hg19: chr1-44403489;