Genetic Variant ENST00000579136.1:n.62-3580_62-3579insT (chr17-40859506-A-AT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000579136.1(ENSG00000265359):n.62-3580_62-3579insT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.84 ( 54064 hom., cov: 0)

Consequence

ENSG00000265359
ENST00000579136.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.761

Publications

1 publications found

Variant links:

Genes affected

ENSG00000265359 (HGNC:):

ENSG00000265359 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371777	XR_934754.3 link	n.63+8655dupT		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265359	ENST00000579136.1 link	n.62-3580_62-3579insT		intron_variant	Intron 1 of 1	3
ENSG00000265359	ENST00000818906.1 link	n.61+8646_61+8647insT		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.844

AC:

126831

AN:

150304

Hom.:

54015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.961

Gnomad AMI

AF:

0.895

Gnomad AMR

AF:

0.846

Gnomad ASJ

AF:

0.807

Gnomad EAS

AF:

0.957

Gnomad SAS

AF:

0.797

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.854

Gnomad NFE

AF:

0.780

Gnomad OTH

AF:

0.832

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

GnomAD4 genome

AF:

0.844

AC:

126935

AN:

150420

Hom.:

54064

Cov.:

AF XY:

0.844

AC XY:

61970

AN XY:

73390

show subpopulations

African (AFR)

AF:

0.961

AC:

39304

AN:

40886

American (AMR)

AF:

0.846

AC:

12761

AN:

15088

Ashkenazi Jewish (ASJ)

AF:

0.807

AC:

2798

AN:

3466

East Asian (EAS)

AF:

0.958

AC:

4891

AN:

5108

South Asian (SAS)

AF:

0.796

AC:

3758

AN:

4724

European-Finnish (FIN)

AF:

0.773

AC:

7949

AN:

10288

Middle Eastern (MID)

AF:

0.847

AC:

249

AN:

294

European-Non Finnish (NFE)

AF:

0.780

AC:

52678

AN:

67566

Other (OTH)

AF:

0.829

AC:

1733

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

910

1820

2729

3639

4549

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

870

1740

2610

3480

4350

<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:

0.723

Hom.:

1423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.76

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