Genetic Variant ENST00000650577.1:n.877+10323C>A (chr17-53426959-G-T) – 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.877+10323C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,082 control chromosomes in the GnomAD database, including 1,629 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 0.14 ( 1629 hom., cov: 32)

Consequence

ENSG00000285939
ENST00000650577.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285939 (HGNC:):

ENSG00000285939 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=-0.93).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 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.877+10323C>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.139

AC:

21101

AN:

151964

Hom.:

1628

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0856

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.0663

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.140

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

GnomAD4 genome

AF:

0.139

AC:

21115

AN:

152082

Hom.:

1629

Cov.:

AF XY:

0.139

AC XY:

10350

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0855

AC:

3547

AN:

41492

American (AMR)

AF:

0.226

AC:

3453

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

535

AN:

3468

East Asian (EAS)

AF:

0.123

AC:

638

AN:

5174

South Asian (SAS)

AF:

0.0664

AC:

320

AN:

4820

European-Finnish (FIN)

AF:

0.143

AC:

1509

AN:

10572

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.155

AC:

10522

AN:

67972

Other (OTH)

AF:

0.140

AC:

295

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

907

1814

2720

3627

4534

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.155

Hom.:

3233

Bravo

AF:

0.149

Asia WGS

AF:

0.0980

AC:

341

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.56

(source)

DANN

Benign

0.45

PhyloP100

0.0

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