rs2118381

Positions:

• chr2-19168317-G-A

Variant summary

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

The ENST00000650025.1(LINC01376):​n.186-42930C>T 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 0.669 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 ENST00000650025.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01376	ENST00000650025.1	n.186-42930C>T		intron_variant, non_coding_transcript_variant
LINC01376	ENST00000418165.5	n.216-42930C>T		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000432142.5	n.233-42930C>T		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000449124.1	n.106-42930C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.673

Alfa AF: 0.738 Hom.: 86092

Bravo AF: 0.651

Asia WGS AF: 0.717 AC: 2485 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2118381; hg19: chr2-19368078;