rs2118381

Variant names:

• chr2-19168317-G-A
• rs2118381
• ENST00000418165.5:n.216-42930C>T

Variant summary

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

The ENST00000449124.1(LINC01376):​n.106-42930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,098 control chromosomes in the GnomAD database, including 35,149 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 0.67 (35149 hom., cov: 34)
• Consequence: LINC01376 ENST00000449124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780
• Publications: 3 publications found

Genes affected

LINC01376 (HGNC:50637): (long intergenic non-protein coding RNA 1376)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449124.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01376	ENST00000418165.5	TSL:4	n.216-42930C>T		intron	N/A
	LINC01376	ENST00000432142.6	TSL:4	n.502-42930C>T		intron	N/A
	LINC01376	ENST00000449124.1	TSL:2	n.106-42930C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101643 AN: 151980 Hom.: 35138 Cov.: 34

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.612

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.669 AC: 101678 AN: 152098 Hom.: 35149 Cov.: 34 AF XY: 0.669 AC XY: 49766 AN XY: 74366

African (AFR) AF: 0.481 AC: 19962 AN: 41460

American (AMR) AF: 0.689 AC: 10524 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3472

East Asian (EAS) AF: 0.680 AC: 3512 AN: 5168

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4826

European-Finnish (FIN) AF: 0.764 AC: 8089 AN: 10590

Middle Eastern (MID) AF: 0.603 AC: 175 AN: 290

European-Non Finnish (NFE) AF: 0.763 AC: 51863 AN: 67990

Other (OTH) AF: 0.673 AC: 1422 AN: 2112

Alfa AF: 0.726 Hom.: 125103

Bravo AF: 0.651

Asia WGS AF: 0.717 AC: 2485 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.61
PhyloP100		-0.078

Splicing

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

Other links and lift over

dbSNP: rs2118381; hg19: chr2-19368078;