chr2-186032920-G-A

Variant names:

• chr2-186032920-G-A
• rs878845
• ENST00000456653.6:n.1050C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456653.6(LINC01473):​n.1050C>T 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 0.67 in 149,984 control chromosomes in the GnomAD database, including 33,773 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 0.67 (33773 hom., cov: 27)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01473 ENST00000456653.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 2 publications found

Genes affected

LINC01473 (HGNC:51109): (long intergenic non-protein coding RNA 1473)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456653.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01473	ENST00000456653.6	TSL:3	n.1050C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC01473	ENST00000655126.2		n.1422C>T		non_coding_transcript_exon	Exon 9 of 9
	LINC01473	ENST00000656786.2		n.1113C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.670 AC: 100460 AN: 149894 Hom.: 33761 Cov.: 27

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.674

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.670 AC: 100504 AN: 149984 Hom.: 33773 Cov.: 27 AF XY: 0.663 AC XY: 48426 AN XY: 73084

African (AFR) AF: 0.618 AC: 25190 AN: 40764

American (AMR) AF: 0.686 AC: 10324 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2543 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2578 AN: 5110

South Asian (SAS) AF: 0.642 AC: 3040 AN: 4734

European-Finnish (FIN) AF: 0.624 AC: 6220 AN: 9966

Middle Eastern (MID) AF: 0.625 AC: 180 AN: 288

European-Non Finnish (NFE) AF: 0.715 AC: 48318 AN: 67602

Other (OTH) AF: 0.668 AC: 1393 AN: 2086

Alfa AF: 0.666 Hom.: 4178

Bravo AF: 0.669

Asia WGS AF: 0.557 AC: 1929 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.66
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs878845; hg19: chr2-186897647;