Genetic Variant ENST00000561320.5:n.222+4469G>C (chr15-38219782-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000561320.5(LINC02895):n.222+4469G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 152,106 control chromosomes in the GnomAD database, including 860 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 0.10 ( 860 hom., cov: 33)

Consequence

LINC02895
ENST00000561320.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730

Publications

7 publications found

Variant links:

Genes affected

LINC02895 (HGNC:55422): (long intergenic non-protein coding RNA 2895)

LINC02895 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=-0.85).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02895	ENST00000561320.5 link	n.222+4469G>C	intron_variant	Intron 2 of 3	1
LINC02895	ENST00000561161.2 link	n.254+4469G>C	intron_variant	Intron 2 of 2	2
LINC02895	ENST00000671149.1 link	n.233+4469G>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0997

AC:

15159

AN:

151988

Hom.:

863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0621

Gnomad AMI

AF:

0.139

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.123

Gnomad EAS

AF:

0.135

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.0493

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.0997

AC:

15161

AN:

152106

Hom.:

860

Cov.:

AF XY:

0.0995

AC XY:

7401

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0620

AC:

2575

AN:

41508

American (AMR)

AF:

0.159

AC:

2429

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

428

AN:

3468

East Asian (EAS)

AF:

0.135

AC:

698

AN:

5176

South Asian (SAS)

AF:

0.144

AC:

694

AN:

4820

European-Finnish (FIN)

AF:

0.0493

AC:

521

AN:

10578

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.109

AC:

7422

AN:

67976

Other (OTH)

AF:

0.108

AC:

228

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

703

1406

2109

2812

3515

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.103

Hom.:

100

Bravo

AF:

0.109

Asia WGS

AF:

0.139

AC:

483

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.2

(source)

DANN

Benign

0.21

PhyloP100

-0.073

Mutation Taster

=100/0

polymorphism

(source)

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