2-19283124-G-T

Variant names:

• chr2-19283124-G-T
• rs703324
• ENST00000418165.5:n.215+22699C>A

Variant summary

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

The ENST00000449124.1(LINC01376):​n.105+63520C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,042 control chromosomes in the GnomAD database, including 13,217 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 0.40 (13217 hom., cov: 32)
• Consequence: LINC01376 ENST00000449124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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 = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01376	ENST00000418165.5	n.215+22699C>A		intron_variant	Intron 1 of 4	4
LINC01376	ENST00000432142.5	n.232+22699C>A		intron_variant	Intron 1 of 4	4
LINC01376	ENST00000449124.1	n.105+63520C>A		intron_variant	Intron 1 of 4	2
LINC01376	ENST00000650025.1	n.185+63520C>A		intron_variant	Intron 2 of 7

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60322 AN: 151922 Hom.: 13199 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.426

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.397 AC: 60381 AN: 152042 Hom.: 13217 Cov.: 32 AF XY: 0.397 AC XY: 29474 AN XY: 74300

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.392

Alfa AF: 0.272 Hom.: 1331

Bravo AF: 0.409

Asia WGS AF: 0.305 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.027
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs703324; hg19: chr2-19482885;