chr2-19283124-G-T

Position:

• chr2-19283124-G-T

Variant summary

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

The ENST00000650025.1(LINC01376):​n.185+63520C>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 0.397 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 ENST00000650025.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01376	ENST00000650025.1	n.185+63520C>A		intron_variant, non_coding_transcript_variant
LINC01376	ENST00000418165.5	n.215+22699C>A		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000432142.5	n.232+22699C>A		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000449124.1	n.105+63520C>A		intron_variant, non_coding_transcript_variant		2

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;