2-150556656-T-C

Variant names:

• chr2-150556656-T-C
• rs1406242
• ENST00000441356.1:n.743A>G

Variant summary

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

The ENST00000441356.1(LINC01920):​n.743A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,062 control chromosomes in the GnomAD database, including 21,732 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 0.49 (21732 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01920 ENST00000441356.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

LINC01920 (HGNC:52738): (long intergenic non-protein coding RNA 1920)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01920	NR_110241.1	n.743A>G		non_coding_transcript_exon_variant	Exon 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01920	ENST00000441356.1	n.743A>G		non_coding_transcript_exon_variant	Exon 5 of 6	1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74362 AN: 151944 Hom.: 21722 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.529

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.489 AC: 74379 AN: 152062 Hom.: 21732 Cov.: 32 AF XY: 0.496 AC XY: 36829 AN XY: 74308

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.663

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.529

Alfa AF: 0.595 Hom.: 53625

Bravo AF: 0.484

Asia WGS AF: 0.639 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406242; hg19: chr2-151413170;