chr1-43937817-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657883.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02918	ENST00000657883.1		n.*101C>A		downstream_gene	N/A
	LINC02918	ENST00000784651.1		n.*79C>A		downstream_gene	N/A
	LINC02918	ENST00000784652.1		n.*79C>A		downstream_gene	N/A

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 v4.9

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;