2-150556656-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441356.1. 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
	LINC01920	NR_110241.1		n.743A>G		non_coding_transcript_exon	Exon 5 of 6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01920	ENST00000441356.1	TSL:1	n.743A>G		non_coding_transcript_exon	Exon 5 of 6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.154 AC: 6379 AN: 41504

American (AMR) AF: 0.663 AC: 10136 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2184 AN: 3466

East Asian (EAS) AF: 0.785 AC: 4057 AN: 5168

South Asian (SAS) AF: 0.608 AC: 2926 AN: 4810

European-Finnish (FIN) AF: 0.580 AC: 6108 AN: 10534

Middle Eastern (MID) AF: 0.572 AC: 166 AN: 290

European-Non Finnish (NFE) AF: 0.599 AC: 40734 AN: 67980

Other (OTH) AF: 0.529 AC: 1118 AN: 2112

Alfa AF: 0.572 Hom.: 82894

Bravo AF: 0.484

Asia WGS AF: 0.639 AC: 2224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.015

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1406242;

hg19: chr2-151413170;