Genetic Variant ENSG00000289601:n.125+74965C>A (chr5-31192521-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 ENST00000523584.1(ENSG00000289601):n.125+74965C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,058 control chromosomes in the GnomAD database, including 3,720 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 0.22 ( 3720 hom., cov: 33)

Consequence

ENSG00000289601
ENST00000523584.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.572

Publications

1 publications found

Variant links:

Genes affected

ENSG00000289601 (HGNC:):

ENSG00000289601 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=-0.55).

BA1

GnomAd4 highest subpopulation (AMR) 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	Effect	Exon rank	TSL
ENSG00000289601	ENST00000523584.1 link	n.125+74965C>A	intron_variant	Intron 1 of 4	5
ENSG00000289601	ENST00000685806.2 link	n.142-17134C>A	intron_variant	Intron 1 of 3
ENSG00000289601	ENST00000692134.1 link	n.274-17134C>A	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

33006

AN:

151940

Hom.:

3719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.171

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.223

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

GnomAD4 genome

AF:

0.217

AC:

33015

AN:

152058

Hom.:

3720

Cov.:

AF XY:

0.217

AC XY:

16148

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.179

AC:

7413

AN:

41476

American (AMR)

AF:

0.253

AC:

3864

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.278

AC:

964

AN:

3470

East Asian (EAS)

AF:

0.172

AC:

886

AN:

5156

South Asian (SAS)

AF:

0.165

AC:

797

AN:

4824

European-Finnish (FIN)

AF:

0.234

AC:

2478

AN:

10572

Middle Eastern (MID)

AF:

0.272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.233

AC:

15864

AN:

67962

Other (OTH)

AF:

0.221

AC:

467

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1331

2662

3992

5323

6654

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.227

Hom.:

6683

Bravo

AF:

0.218

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

7.9

(source)

DANN

Benign

0.64

PhyloP100

-0.57

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