Genetic Variant ENST00000662475.1:n.307+2374G>T (chr4-87986984-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000662475.1(ENSG00000286618):n.307+2374G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,924 control chromosomes in the GnomAD database, including 9,516 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 0.34 ( 9516 hom., cov: 32)

Consequence

ENSG00000286618
ENST00000662475.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0290

Publications

7 publications found

Variant links:

Genes affected

ENSG00000286618 (HGNC:):

ENSG00000286618 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.406 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
ENSG00000286618	ENST00000662475.1 link	n.307+2374G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.343

AC:

52128

AN:

151806

Hom.:

9511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.377

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.349

Gnomad OTH

AF:

0.333

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

GnomAD4 genome

AF:

0.343

AC:

52163

AN:

151924

Hom.:

9516

Cov.:

AF XY:

0.340

AC XY:

25276

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.412

AC:

17043

AN:

41400

American (AMR)

AF:

0.271

AC:

4141

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.302

AC:

1048

AN:

3468

East Asian (EAS)

AF:

0.00212

AC:

AN:

5182

South Asian (SAS)

AF:

0.225

AC:

1084

AN:

4814

European-Finnish (FIN)

AF:

0.380

AC:

3991

AN:

10510

Middle Eastern (MID)

AF:

0.293

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.349

AC:

23722

AN:

67952

Other (OTH)

AF:

0.329

AC:

693

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1718

3436

5153

6871

8589

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.353

Hom.:

1181

Bravo

AF:

0.334

Asia WGS

AF:

0.131

AC:

454

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

(source)

DANN

Benign

0.14

PhyloP100

-0.029

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