Genetic Variant ENSG00000304533:n.368+1253T>C (chr2-102291170-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 ENST00000804381.1(ENSG00000304533):n.368+1253T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 151,946 control chromosomes in the GnomAD database, including 34,403 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 0.67 ( 34403 hom., cov: 30)

Consequence

ENSG00000304533
ENST00000804381.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.16

Publications

6 publications found

Variant links:

Genes affected

ENSG00000304533 (HGNC:):

ENSG00000304533 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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
ENSG00000304533	ENST00000804381.1 link	n.368+1253T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.668

AC:

101447

AN:

151828

Hom.:

34369

Cov.:

show subpopulations

Gnomad AFR

AF:

0.603

Gnomad AMI

AF:

0.649

Gnomad AMR

AF:

0.725

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.972

Gnomad SAS

AF:

0.751

Gnomad FIN

AF:

0.733

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.660

Gnomad OTH

AF:

0.664

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

GnomAD4 genome

AF:

0.668

AC:

101531

AN:

151946

Hom.:

34403

Cov.:

AF XY:

0.676

AC XY:

50174

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.603

AC:

24964

AN:

41416

American (AMR)

AF:

0.725

AC:

11066

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.602

AC:

2086

AN:

3466

East Asian (EAS)

AF:

0.972

AC:

5034

AN:

5178

South Asian (SAS)

AF:

0.750

AC:

3598

AN:

4800

European-Finnish (FIN)

AF:

0.733

AC:

7746

AN:

10566

Middle Eastern (MID)

AF:

0.627

AC:

183

AN:

292

European-Non Finnish (NFE)

AF:

0.660

AC:

44857

AN:

67952

Other (OTH)

AF:

0.668

AC:

1406

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1685

3369

5054

6738

8423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.664

Hom.:

10437

Bravo

AF:

0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.068

(source)

DANN

Benign

0.32

PhyloP100

-3.2

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