Genetic Variant ENSG00000284999:n.281+24933A>G (chr6-105805124-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 ENST00000644129.1(ENSG00000284999):n.281+24933A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,048 control chromosomes in the GnomAD database, including 10,447 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 0.36 ( 10447 hom., cov: 33)

Consequence

ENSG00000284999
ENST00000644129.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.112

Publications

7 publications found

Variant links:

Genes affected

ENSG00000284999 (HGNC:):

ENSG00000284999 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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
ENSG00000284999	ENST00000644129.1 link	n.281+24933A>G		intron_variant	Intron 3 of 3
ENSG00000284999	ENST00000744159.1 link	n.374+24933A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54642

AN:

151930

Hom.:

10433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.490

Gnomad AMI

AF:

0.326

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.310

Gnomad OTH

AF:

0.339

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

GnomAD4 genome

AF:

0.360

AC:

54703

AN:

152048

Hom.:

10447

Cov.:

AF XY:

0.359

AC XY:

26677

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.490

AC:

20315

AN:

41458

American (AMR)

AF:

0.253

AC:

3864

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

956

AN:

3470

East Asian (EAS)

AF:

0.375

AC:

1941

AN:

5170

South Asian (SAS)

AF:

0.389

AC:

1877

AN:

4826

European-Finnish (FIN)

AF:

0.338

AC:

3562

AN:

10552

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.310

AC:

21094

AN:

67978

Other (OTH)

AF:

0.339

AC:

715

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1745

3490

5236

6981

8726

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

526

1052

1578

2104

2630

<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:

0.331

Hom.:

13793

Bravo

AF:

0.358

Asia WGS

AF:

0.378

AC:

1311

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.5

(source)

DANN

Benign

0.57

PhyloP100

0.11

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