Genetic Variant ENSG00000308413:n.513T>G (chr18-21112383-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000833849.1(ENSG00000308413):n.513T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,162 control chromosomes in the GnomAD database, including 6,831 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 0.28 ( 6831 hom., cov: 33)

Consequence

ENSG00000308413
ENST00000833849.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0360

Publications

21 publications found

Variant links:

Genes affected

ENSG00000308413 (HGNC:):

ENSG00000308413 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=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000308413	ENST00000833849.1 link	n.513T>G	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000308413	ENST00000833850.1 link	n.440T>G	non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000308413	ENST00000833851.1 link	n.196T>G	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.278

AC:

42306

AN:

152042

Hom.:

6814

Cov.:

show subpopulations

Gnomad AFR

AF:

0.440

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.327

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.0897

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.293

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

GnomAD4 genome

AF:

0.279

AC:

42386

AN:

152162

Hom.:

6831

Cov.:

AF XY:

0.275

AC XY:

20474

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.441

AC:

18295

AN:

41520

American (AMR)

AF:

0.327

AC:

5000

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.293

AC:

1015

AN:

3470

East Asian (EAS)

AF:

0.0905

AC:

468

AN:

5170

South Asian (SAS)

AF:

0.141

AC:

679

AN:

4830

European-Finnish (FIN)

AF:

0.188

AC:

1993

AN:

10580

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

14037

AN:

67984

Other (OTH)

AF:

0.291

AC:

615

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1532

3064

4596

6128

7660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.246

Hom.:

868

Bravo

AF:

0.298

Asia WGS

AF:

0.146

AC:

506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

(source)

DANN

Benign

0.66

PhyloP100

0.036

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