Genetic Variant ENSG00000285681:n.113+38626T>G (chr18-60367971-T-G) – 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+38626T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0675 in 152,130 control chromosomes in the GnomAD database, including 489 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 0.067 ( 489 hom., cov: 33)

Consequence

ENSG00000285681
ENST00000650201.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45

Publications

18 publications found

Variant links:

Genes affected

ENSG00000285681 (HGNC:):

ENSG00000285681 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 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+38626T>G		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1 link	n.156+38626T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0675

AC:

10264

AN:

152012

Hom.:

489

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0152

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.0461

Gnomad ASJ

AF:

0.0959

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0951

Gnomad OTH

AF:

0.0622

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

GnomAD4 genome

AF:

0.0675

AC:

10262

AN:

152130

Hom.:

489

Cov.:

AF XY:

0.0665

AC XY:

4950

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0152

AC:

629

AN:

41518

American (AMR)

AF:

0.0460

AC:

703

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0959

AC:

332

AN:

3462

East Asian (EAS)

AF:

0.00155

AC:

AN:

5170

South Asian (SAS)

AF:

0.125

AC:

602

AN:

4802

European-Finnish (FIN)

AF:

0.125

AC:

1324

AN:

10588

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0950

AC:

6461

AN:

67976

Other (OTH)

AF:

0.0616

AC:

130

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

480

960

1441

1921

2401

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0811

Hom.:

974

Bravo

AF:

0.0586

Asia WGS

AF:

0.0420

AC:

144

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.38

(source)

DANN

Benign

0.56

PhyloP100

-1.4

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