Genetic Variant ENSG00000299064:n.344-5737A>G (chr2-105459653-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 ENST00000760277.1(ENSG00000299064):n.344-5737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,974 control chromosomes in the GnomAD database, including 2,961 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 0.18 ( 2961 hom., cov: 31)

Consequence

ENSG00000299064
ENST00000760277.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.399

Publications

1 publications found

Variant links:

Genes affected

ENSG00000299064 (HGNC:):

ENSG00000299064 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000299064	ENST00000760277.1 link	n.344-5737A>G	intron_variant	Intron 1 of 2
ENSG00000299064	ENST00000760278.1 link	n.344-5737A>G	intron_variant	Intron 1 of 1
ENSG00000299064	ENST00000760279.1 link	n.117-5737A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

27918

AN:

151852

Hom.:

2953

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.168

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.170

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

GnomAD4 genome

AF:

0.184

AC:

27962

AN:

151974

Hom.:

2961

Cov.:

AF XY:

0.184

AC XY:

13676

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.287

AC:

11889

AN:

41436

American (AMR)

AF:

0.206

AC:

3140

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

375

AN:

3470

East Asian (EAS)

AF:

0.168

AC:

868

AN:

5180

South Asian (SAS)

AF:

0.170

AC:

816

AN:

4802

European-Finnish (FIN)

AF:

0.135

AC:

1425

AN:

10526

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.131

AC:

8896

AN:

67990

Other (OTH)

AF:

0.176

AC:

373

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1104

2207

3311

4414

5518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.148

Hom.:

3478

Bravo

AF:

0.192

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.70

(source)

DANN

Benign

0.48

PhyloP100

-0.40

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