rs851426

Positions:

• chr2-19293214-A-T

Variant summary

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

The ENST00000650025.1(LINC01376):​n.185+53430T>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 0.312 in 151,986 control chromosomes in the GnomAD database, including 8,424 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 0.31 (8424 hom., cov: 32)
• Consequence: LINC01376 ENST00000650025.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01376	ENST00000650025.1	n.185+53430T>A		intron_variant, non_coding_transcript_variant
LINC01376	ENST00000418165.5	n.215+12609T>A		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000432142.5	n.232+12609T>A		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000449124.1	n.105+53430T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47331 AN: 151868 Hom.: 8413 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.312 AC: 47385 AN: 151986 Hom.: 8424 Cov.: 32 AF XY: 0.312 AC XY: 23170 AN XY: 74316

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.296

Alfa AF: 0.268 Hom.: 789

Bravo AF: 0.312

Asia WGS AF: 0.235 AC: 815 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs851426; hg19: chr2-19492975;