Genetic Variant ENSG00000287849:n.1171-3519A>G (chr2-18496421-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 ENST00000668609.2(ENSG00000287849):n.1171-3519A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,132 control chromosomes in the GnomAD database, including 5,504 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 0.26 ( 5504 hom., cov: 32)

Consequence

ENSG00000287849
ENST00000668609.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.292

Publications

3 publications found

Variant links:

Genes affected

ENSG00000287849 (HGNC:):

ENSG00000287849 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373454	XR_001739302.1 link	n.815+3754T>C		intron_variant	Intron 5 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287849	ENST00000668609.2 link	n.1171-3519A>G	intron_variant	Intron 3 of 4
ENSG00000287881	ENST00000670548.1 link	n.197+3754T>C	intron_variant	Intron 2 of 2
ENSG00000287849	ENST00000690447.2 link	n.271-3519A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39108

AN:

152014

Hom.:

5506

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.375

Gnomad AMR

AF:

0.211

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.0148

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.258

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

GnomAD4 genome

AF:

0.257

AC:

39118

AN:

152132

Hom.:

5504

Cov.:

AF XY:

0.249

AC XY:

18551

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.202

AC:

8371

AN:

41510

American (AMR)

AF:

0.211

AC:

3219

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1213

AN:

3466

East Asian (EAS)

AF:

0.0146

AC:

AN:

5188

South Asian (SAS)

AF:

0.155

AC:

750

AN:

4828

European-Finnish (FIN)

AF:

0.246

AC:

2598

AN:

10570

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.322

AC:

21885

AN:

67972

Other (OTH)

AF:

0.255

AC:

539

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1454

2909

4363

5818

7272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

396

792

1188

1584

1980

<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:

0.151

Hom.:

404

Bravo

AF:

0.253

Asia WGS

AF:

0.0900

AC:

313

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

3.9

(source)

DANN

Benign

0.45

PhyloP100

0.29

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