Genetic Variant ENSG00000306102:n.440-2792G>T (chr13-22654552-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 ENST00000815334.1(ENSG00000306102):n.440-2792G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,994 control chromosomes in the GnomAD database, including 12,618 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 0.38 ( 12618 hom., cov: 32)

Consequence

ENSG00000306102
ENST00000815334.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0720

Publications

27 publications found

Variant links:

Genes affected

ENSG00000306102 (HGNC:):

ENSG00000306102 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 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
ENSG00000306102	ENST00000815334.1 link	n.440-2792G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.382

AC:

58005

AN:

151874

Hom.:

12595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.598

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.413

Gnomad MID

AF:

0.318

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.356

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

GnomAD4 genome

AF:

0.382

AC:

58076

AN:

151994

Hom.:

12618

Cov.:

AF XY:

0.382

AC XY:

28371

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.598

AC:

24796

AN:

41436

American (AMR)

AF:

0.300

AC:

4583

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

870

AN:

3472

East Asian (EAS)

AF:

0.334

AC:

1728

AN:

5174

South Asian (SAS)

AF:

0.213

AC:

1025

AN:

4814

European-Finnish (FIN)

AF:

0.413

AC:

4359

AN:

10546

Middle Eastern (MID)

AF:

0.320

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.289

AC:

19667

AN:

67966

Other (OTH)

AF:

0.357

AC:

753

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1705

3411

5116

6822

8527

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

528

1056

1584

2112

2640

<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:

0.307

Hom.:

34868

Bravo

AF:

0.382

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.46

PhyloP100

-0.072

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