Genetic Variant ENST00000650201.1:n.113+20845G>A (chr18-60350190-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000650201.1(ENSG00000285681):n.113+20845G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 152,240 control chromosomes in the GnomAD database, including 142 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 0.035 ( 142 hom., cov: 32)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0700

Publications

2 publications found

Variant links:

Genes affected

ENSG00000285681 (HGNC:):

ENSG00000285681 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0545 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
ENSG00000285681	ENST00000650201.1 link	n.113+20845G>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.156+20845G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0352

AC:

5358

AN:

152122

Hom.:

142

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00956

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0365

Gnomad ASJ

AF:

0.0643

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00580

Gnomad FIN

AF:

0.0188

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0560

Gnomad OTH

AF:

0.0474

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

GnomAD4 genome

AF:

0.0352

AC:

5355

AN:

152240

Hom.:

142

Cov.:

AF XY:

0.0319

AC XY:

2378

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.00951

AC:

395

AN:

41542

American (AMR)

AF:

0.0364

AC:

556

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0643

AC:

223

AN:

3468

East Asian (EAS)

AF:

0.000579

AC:

AN:

5178

South Asian (SAS)

AF:

0.00581

AC:

AN:

4820

European-Finnish (FIN)

AF:

0.0188

AC:

199

AN:

10608

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0560

AC:

3808

AN:

68016

Other (OTH)

AF:

0.0469

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

262

525

787

1050

1312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0499

Hom.:

290

Bravo

AF:

0.0362

Asia WGS

AF:

0.00751

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.8

(source)

DANN

Benign

0.75

PhyloP100

0.070

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