Genetic Variant ENST00000700882.2:n.237-4418T>G (chr3-115762715-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 ENST00000700882.2(ENSG00000289153):n.237-4418T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,126 control chromosomes in the GnomAD database, including 2,366 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 0.17 ( 2366 hom., cov: 32)

Consequence

ENSG00000289153
ENST00000700882.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.92

Publications

4 publications found

Variant links:

Genes affected

ENSG00000289153 (HGNC:):

ENSG00000289153 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000289153	ENST00000700882.2 link	n.237-4418T>G	intron_variant	Intron 1 of 1
ENSG00000289153	ENST00000750609.1 link	n.208+29585T>G	intron_variant	Intron 1 of 1
ENSG00000289153	ENST00000750610.1 link	n.285-4418T>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25672

AN:

152008

Hom.:

2353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.152

Gnomad SAS

AF:

0.118

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.165

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

GnomAD4 genome

AF:

0.169

AC:

25721

AN:

152126

Hom.:

2366

Cov.:

AF XY:

0.173

AC XY:

12862

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.214

AC:

8885

AN:

41502

American (AMR)

AF:

0.239

AC:

3645

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

403

AN:

3470

East Asian (EAS)

AF:

0.153

AC:

791

AN:

5176

South Asian (SAS)

AF:

0.119

AC:

572

AN:

4818

European-Finnish (FIN)

AF:

0.200

AC:

2112

AN:

10574

Middle Eastern (MID)

AF:

0.160

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.130

AC:

8814

AN:

67988

Other (OTH)

AF:

0.164

AC:

346

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1068

2136

3204

4272

5340

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.164

Hom.:

435

Bravo

AF:

0.171

Asia WGS

AF:

0.137

AC:

477

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.4

(source)

DANN

Benign

0.69

PhyloP100

1.9

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