Genetic Variant ENSG00000286533:n.42+91950A>G (chr6-159570636-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000656085.1(ENSG00000286533):n.42+91950A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,096 control chromosomes in the GnomAD database, including 2,305 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 0.17 ( 2305 hom., cov: 32)

Consequence

ENSG00000286533
ENST00000656085.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0580

Publications

2 publications found

Variant links:

Genes affected

ENSG00000286533 (HGNC:):

ENSG00000286533 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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
ENSG00000286533	ENST00000656085.1 link	n.42+91950A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25292

AN:

151978

Hom.:

2302

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.143

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

GnomAD4 genome

AF:

0.166

AC:

25311

AN:

152096

Hom.:

2305

Cov.:

AF XY:

0.167

AC XY:

12446

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.250

AC:

10343

AN:

41432

American (AMR)

AF:

0.130

AC:

1985

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.105

AC:

364

AN:

3472

East Asian (EAS)

AF:

0.175

AC:

906

AN:

5166

South Asian (SAS)

AF:

0.202

AC:

976

AN:

4822

European-Finnish (FIN)

AF:

0.142

AC:

1505

AN:

10588

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.130

AC:

8863

AN:

67994

Other (OTH)

AF:

0.143

AC:

302

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1068

2137

3205

4274

5342

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.152

Hom.:

326

Bravo

AF:

0.166

Asia WGS

AF:

0.187

AC:

648

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

4.0

(source)

DANN

Benign

0.37

PhyloP100

-0.058

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