Genetic Variant ENST00000615847.3:n.2056T>A (chr21-44934070-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000615847.3(LINC01547):n.2056T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

LINC01547
ENST00000615847.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.164

Publications

6 publications found

Variant links:

Genes affected

LINC01547 (HGNC:15707): (long intergenic non-protein coding RNA 1547) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

LINC01547 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01547	NR_027128.1 link	n.1047T>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01547	ENST00000615847.3 link	n.2056T>A	non_coding_transcript_exon_variant	Exon 4 of 4	1
LINC01547	ENST00000397841.5 link	n.1047T>A	non_coding_transcript_exon_variant	Exon 4 of 4	2
LINC01547	ENST00000654166.2 link	n.2224T>A	non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

210384

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

115782

African (AFR)

AF:

0.00

AC:

AN:

5246

American (AMR)

AF:

0.00

AC:

AN:

11686

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

4202

East Asian (EAS)

AF:

0.00

AC:

AN:

8322

South Asian (SAS)

AF:

0.00

AC:

AN:

42350

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20748

Middle Eastern (MID)

AF:

0.00

AC:

AN:

680

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

107712

Other (OTH)

AF:

0.00

AC:

AN:

9438

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1396

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.0

(source)

DANN

Benign

0.46

PhyloP100

-0.16

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over