Genetic Variant ENST00000554732.5:n.222-2614C>T (chr14-38841818-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000554732.5(LINC00639):n.222-2614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,102 control chromosomes in the GnomAD database, including 1,917 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 0.14 ( 1917 hom., cov: 32)

Consequence

LINC00639
ENST00000554732.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193

Publications

4 publications found

Variant links:

Genes affected

LINC00639 (HGNC:27502): (long intergenic non-protein coding RNA 639)

LINC00639 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=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00639	NR_039982.1 link	n.160-2614C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00639	ENST00000554732.5 link	n.222-2614C>T	intron_variant	Intron 3 of 5	1
LINC00639	ENST00000553932.5 link	n.155-2614C>T	intron_variant	Intron 2 of 6	2
LINC00639	ENST00000556116.2 link	n.246-2614C>T	intron_variant	Intron 2 of 7	4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

21972

AN:

151984

Hom.:

1913

Cov.:

show subpopulations

Gnomad AFR

AF:

0.143

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.145

AC:

22007

AN:

152102

Hom.:

1917

Cov.:

AF XY:

0.150

AC XY:

11175

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.143

AC:

5925

AN:

41488

American (AMR)

AF:

0.300

AC:

4589

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

531

AN:

3468

East Asian (EAS)

AF:

0.102

AC:

528

AN:

5172

South Asian (SAS)

AF:

0.162

AC:

782

AN:

4830

European-Finnish (FIN)

AF:

0.139

AC:

1465

AN:

10550

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7597

AN:

67988

Other (OTH)

AF:

0.175

AC:

369

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

947

1894

2840

3787

4734

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.129

Hom.:

2308

Bravo

AF:

0.161

Asia WGS

AF:

0.142

AC:

495

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.66

(source)

DANN

Benign

0.28

PhyloP100

-0.19

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over