rs851426

Variant names:

• chr2-19293214-A-T
• rs851426
• ENST00000418165.5:n.215+12609T>A

Variant summary

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

The ENST00000449124.1(LINC01376):​n.105+53430T>A variant causes a intron 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 ENST00000449124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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.215+12609T>A		intron	N/A
	LINC01376	ENST00000432142.6	TSL:4	n.501+12609T>A		intron	N/A
	LINC01376	ENST00000449124.1	TSL:2	n.105+53430T>A		intron	N/A

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

African (AFR) AF: 0.501 AC: 20759 AN: 41426

American (AMR) AF: 0.231 AC: 3533 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1229 AN: 5180

South Asian (SAS) AF: 0.296 AC: 1424 AN: 4818

European-Finnish (FIN) AF: 0.293 AC: 3098 AN: 10556

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.227 AC: 15408 AN: 67952

Other (OTH) AF: 0.296 AC: 623 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.60
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs851426; hg19: chr2-19492975;