Genetic Variant ENST00000434081.1:n.183+174T>C (chr21-44993730-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000434081.1(LINC00163):n.183+174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 148,984 control chromosomes in the GnomAD database, including 584 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 0.082 ( 584 hom., cov: 31)

Consequence

LINC00163
ENST00000434081.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.57

Publications

1 publications found

Variant links:

Genes affected

LINC00163 (HGNC:33165): (long intergenic non-protein coding RNA 163)

LINC00163 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00163	NR_033840.1 link	n.183+174T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00163	ENST00000434081.1 link	n.183+174T>C		intron_variant	Intron 1 of 1	1
LINC00163	ENST00000439088.1 link	n.166+174T>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.0822

AC:

12237

AN:

148876

Hom.:

582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0499

Gnomad AMI

AF:

0.108

Gnomad AMR

AF:

0.0712

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.0239

Gnomad SAS

AF:

0.0678

Gnomad FIN

AF:

0.0812

Gnomad MID

AF:

0.194

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.0940

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

GnomAD4 genome

AF:

0.0821

AC:

12235

AN:

148984

Hom.:

584

Cov.:

AF XY:

0.0791

AC XY:

5753

AN XY:

72688

show subpopulations

African (AFR)

AF:

0.0498

AC:

2006

AN:

40296

American (AMR)

AF:

0.0709

AC:

1066

AN:

15026

Ashkenazi Jewish (ASJ)

AF:

0.127

AC:

437

AN:

3448

East Asian (EAS)

AF:

0.0240

AC:

121

AN:

5042

South Asian (SAS)

AF:

0.0684

AC:

315

AN:

4606

European-Finnish (FIN)

AF:

0.0812

AC:

834

AN:

10268

Middle Eastern (MID)

AF:

0.208

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.106

AC:

7107

AN:

67034

Other (OTH)

AF:

0.0926

AC:

192

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

566

1132

1698

2264

2830

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0975

Hom.:

219

Bravo

AF:

0.0779

Asia WGS

AF:

0.0560

AC:

194

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

(source)

DANN

Benign

0.60

PhyloP100

-4.6

Splicing

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

Publications

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ENST00000434081.1:n.183+174T>C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over