Genetic Variant ENST00000417751.5:n.308-36394T>G (chr2-13775678-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000417751.5(LINC00276):n.308-36394T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,004 control chromosomes in the GnomAD database, including 17,060 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 0.43 ( 17060 hom., cov: 32)

Consequence

LINC00276
ENST00000417751.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.422

Publications

0 publications found

Variant links:

Genes affected

LINC00276 (HGNC:38663): (long intergenic non-protein coding RNA 276)

LINC00276 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 = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00276	ENST00000417751.5 link	n.308-36394T>G		intron_variant	Intron 3 of 4	2
LINC00276	ENST00000747982.1 link	n.52-64957T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.431

AC:

65390

AN:

151886

Hom.:

17056

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.654

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.336

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.490

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.465

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

GnomAD4 genome

AF:

0.430

AC:

65404

AN:

152004

Hom.:

17060

Cov.:

AF XY:

0.428

AC XY:

31800

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.135

AC:

5602

AN:

41518

American (AMR)

AF:

0.537

AC:

8200

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.458

AC:

1590

AN:

3470

East Asian (EAS)

AF:

0.277

AC:

1432

AN:

5166

South Asian (SAS)

AF:

0.335

AC:

1614

AN:

4816

European-Finnish (FIN)

AF:

0.527

AC:

5547

AN:

10524

Middle Eastern (MID)

AF:

0.507

AC:

148

AN:

292

European-Non Finnish (NFE)

AF:

0.584

AC:

39698

AN:

67932

Other (OTH)

AF:

0.465

AC:

977

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1616

3232

4849

6465

8081

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<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:

0.529

Hom.:

11364

Bravo

AF:

0.422

Asia WGS

AF:

0.300

AC:

1043

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

0.95

(source)

DANN

Benign

0.62

PhyloP100

-0.42

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