Genetic Variant ENSG00000289487:n.542-36385T>A (chr10-62852354-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000493899.2(ENSG00000289487):n.542-36385T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,894 control chromosomes in the GnomAD database, including 17,500 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 0.48 ( 17500 hom., cov: 31)

Consequence

ENSG00000289487
ENST00000493899.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.564

Publications

4 publications found

Variant links:

Genes affected

ENSG00000289487 (HGNC:):

ENSG00000289487 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 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
ENSG00000289487	ENST00000493899.2 link	n.542-36385T>A		intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.478

AC:

72516

AN:

151776

Hom.:

17488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.428

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.420

Gnomad ASJ

AF:

0.473

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.518

Gnomad OTH

AF:

0.476

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

GnomAD4 genome

AF:

0.478

AC:

72575

AN:

151894

Hom.:

17500

Cov.:

AF XY:

0.481

AC XY:

35729

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.428

AC:

17738

AN:

41420

American (AMR)

AF:

0.420

AC:

6403

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.473

AC:

1640

AN:

3470

East Asian (EAS)

AF:

0.391

AC:

2022

AN:

5168

South Asian (SAS)

AF:

0.491

AC:

2360

AN:

4810

European-Finnish (FIN)

AF:

0.532

AC:

5595

AN:

10520

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.518

AC:

35208

AN:

67946

Other (OTH)

AF:

0.477

AC:

1002

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1918

3835

5753

7670

9588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

666

1332

1998

2664

3330

<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:

0.388

Hom.:

1112

Bravo

AF:

0.463

Asia WGS

AF:

0.469

AC:

1626

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.0

(source)

DANN

Benign

0.82

PhyloP100

0.56

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