2-19121042-T-C

Position:

• chr2-19121042-T-C

Variant summary

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

The ENST00000650025.1(LINC01376):​n.321+4210A>G 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 0.586 in 152,002 control chromosomes in the GnomAD database, including 26,755 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 0.59 (26755 hom., cov: 32)
• Consequence: LINC01376 ENST00000650025.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 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.321+4210A>G		intron_variant, non_coding_transcript_variant
LINC01376	ENST00000418165.5	n.351+4210A>G		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000432142.5	n.368+4210A>G		intron_variant, non_coding_transcript_variant		4
LINC01376	ENST00000449124.1	n.241+4210A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88960 AN: 151884 Hom.: 26732 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.586 AC: 89031 AN: 152002 Hom.: 26755 Cov.: 32 AF XY: 0.585 AC XY: 43435 AN XY: 74280

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.607

Alfa AF: 0.614 Hom.: 10401

Bravo AF: 0.587

Asia WGS AF: 0.568 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12710696; hg19: chr2-19320803;