Genetic Variant ENST00000837048.1:n.752-212G>A (chr10-8930055-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 ENST00000837048.1(LINC02676):n.752-212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,064 control chromosomes in the GnomAD database, including 2,752 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 0.15 ( 2752 hom., cov: 32)

Consequence

LINC02676
ENST00000837048.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

40 publications found

Variant links:

Genes affected

LINC02676 (HGNC:54170): (long intergenic non-protein coding RNA 2676)

LINC02676 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=-1.07).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02676	ENST00000837048.1 link	n.752-212G>A	intron_variant	Intron 1 of 4
LINC02676	ENST00000837049.1 link	n.716-14043G>A	intron_variant	Intron 1 of 4
LINC02676	ENST00000837050.1 link	n.704-36488G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22382

AN:

151946

Hom.:

2742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.0418

Gnomad AMR

AF:

0.218

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.270

Gnomad FIN

AF:

0.0604

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.0697

Gnomad OTH

AF:

0.159

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

GnomAD4 genome

AF:

0.148

AC:

22432

AN:

152064

Hom.:

2752

Cov.:

AF XY:

0.154

AC XY:

11473

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.196

AC:

8123

AN:

41450

American (AMR)

AF:

0.218

AC:

3339

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

627

AN:

3466

East Asian (EAS)

AF:

0.622

AC:

3204

AN:

5150

South Asian (SAS)

AF:

0.270

AC:

1300

AN:

4806

European-Finnish (FIN)

AF:

0.0604

AC:

640

AN:

10598

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0697

AC:

4741

AN:

67998

Other (OTH)

AF:

0.166

AC:

349

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

861

1721

2582

3442

4303

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.101

Hom.:

5530

Bravo

AF:

0.161

Asia WGS

AF:

0.433

AC:

1505

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.20

(source)

DANN

Benign

0.77

PhyloP100

-1.2

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