Genetic Variant ENSG00000285939:n.660-38434T>C (chr17-53483508-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000650577.1(ENSG00000285939):n.660-38434T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 152,066 control chromosomes in the GnomAD database, including 306 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 0.051 ( 306 hom., cov: 32)

Consequence

ENSG00000285939
ENST00000650577.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285939 (HGNC:):

ENSG00000285939 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 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
ENSG00000285939	ENST00000650577.1 link	n.660-38434T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.0512

AC:

7787

AN:

151948

Hom.:

305

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0324

Gnomad ASJ

AF:

0.0300

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0602

Gnomad FIN

AF:

0.0171

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0286

Gnomad OTH

AF:

0.0393

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

GnomAD4 genome

AF:

0.0513

AC:

7802

AN:

152066

Hom.:

306

Cov.:

AF XY:

0.0507

AC XY:

3768

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.111

AC:

4629

AN:

41532

American (AMR)

AF:

0.0323

AC:

494

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0300

AC:

104

AN:

3464

East Asian (EAS)

AF:

0.00135

AC:

AN:

5186

South Asian (SAS)

AF:

0.0607

AC:

293

AN:

4826

European-Finnish (FIN)

AF:

0.0171

AC:

181

AN:

10614

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0286

AC:

1941

AN:

67854

Other (OTH)

AF:

0.0389

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

364

727

1091

1454

1818

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0349

Hom.:

Bravo

AF:

0.0553

Asia WGS

AF:

0.0440

AC:

153

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.70

(source)

DANN

Benign

0.44

PhyloP100

-0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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