Genetic Variant ENST00000512839.5:n.99-5968T>C (chr4-188430736-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000512839.5(LINC01060):n.99-5968T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,072 control chromosomes in the GnomAD database, including 5,791 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 0.27 ( 5791 hom., cov: 32)

Consequence

LINC01060
ENST00000512839.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.936

Variant links:

Genes affected

LINC01060 (HGNC:49081): (long intergenic non-protein coding RNA 1060)

LINC01060 links:

LOC105377609 (HGNC:):

LOC105377609 links:

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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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377609	XR_001741960.2 link	n.4747A>G		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105377609	XR_939621.3 link	n.4735A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01060	ENST00000512839.5 link	n.99-5968T>C	intron_variant	Intron 1 of 4	1
LINC01060	ENST00000513313.5 link	n.99-5968T>C	intron_variant	Intron 1 of 2	5
LINC01060	ENST00000806916.1 link	n.266-5968T>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.266

AC:

40472

AN:

151954

Hom.:

5786

Cov.:

show subpopulations

Gnomad AFR

AF:

0.365

Gnomad AMI

AF:

0.252

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.224

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

GnomAD4 genome

AF:

0.266

AC:

40501

AN:

152072

Hom.:

5791

Cov.:

AF XY:

0.264

AC XY:

19658

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.365

AC:

15141

AN:

41466

American (AMR)

AF:

0.231

AC:

3525

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

957

AN:

3470

East Asian (EAS)

AF:

0.373

AC:

1928

AN:

5168

South Asian (SAS)

AF:

0.255

AC:

1228

AN:

4822

European-Finnish (FIN)

AF:

0.218

AC:

2301

AN:

10566

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14681

AN:

67982

Other (OTH)

AF:

0.222

AC:

469

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1469

2938

4408

5877

7346

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.242

Hom.:

619

Bravo

AF:

0.271

Asia WGS

AF:

0.253

AC:

879

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.2

(source)

DANN

Benign

0.50

PhyloP100

-0.94

Splicing

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

Publications

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ENST00000512839.5:n.99-5968T>C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over