Genetic Variant ENSG00000285534:n.759-33045C>G (chr13-109604203-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000650264.1(ENSG00000285534):n.759-33045C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,116 control chromosomes in the GnomAD database, including 4,323 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 0.22 ( 4323 hom., cov: 32)

Consequence

ENSG00000285534
ENST00000650264.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00300

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285534 (HGNC:):

ENSG00000285534 links:

Genome browser will be placed here

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1 link	n.940+2006C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285534	ENST00000650264.1 link	n.759-33045C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32853

AN:

151998

Hom.:

4321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.540

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.225

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

GnomAD4 genome

AF:

0.216

AC:

32862

AN:

152116

Hom.:

4323

Cov.:

AF XY:

0.227

AC XY:

16870

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.128

AC:

5294

AN:

41502

American (AMR)

AF:

0.316

AC:

4825

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

635

AN:

3470

East Asian (EAS)

AF:

0.539

AC:

2775

AN:

5144

South Asian (SAS)

AF:

0.421

AC:

2025

AN:

4812

European-Finnish (FIN)

AF:

0.250

AC:

2639

AN:

10570

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.206

AC:

13996

AN:

68010

Other (OTH)

AF:

0.227

AC:

481

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1259

2518

3777

5036

6295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

364

728

1092

1456

1820

<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:

0.110

Hom.:

192

Bravo

AF:

0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.51

(source)

DANN

Benign

0.40

PhyloP100

-0.0030

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