Genetic Variant ENSG00000290217:c.703-9986_703-9985insT (chr6-25708782-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The ENST00000703602.1(ENSG00000290217):c.703-9986_703-9985insT 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 0.82 ( 50143 hom., cov: 0)

Consequence

ENSG00000290217
ENST00000703602.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.377

Publications

5 publications found

Variant links:

Genes affected

ENSG00000290217 (HGNC:):

ENSG00000290217 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703602.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290217	ENST00000703602.1		c.703-9986_703-9985insT		intron	N/A	ENSP00000515390.1	A0A994J4C2

Frequencies

GnomAD3 genomes

AF:

0.823

AC:

121606

AN:

147768

Hom.:

50129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.760

Gnomad AMI

AF:

0.963

Gnomad AMR

AF:

0.855

Gnomad ASJ

AF:

0.775

Gnomad EAS

AF:

0.936

Gnomad SAS

AF:

0.849

Gnomad FIN

AF:

0.792

Gnomad MID

AF:

0.747

Gnomad NFE

AF:

0.849

Gnomad OTH

AF:

0.798

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

GnomAD4 genome

AF:

0.823

AC:

121651

AN:

147840

Hom.:

50143

Cov.:

AF XY:

0.821

AC XY:

58976

AN XY:

71834

show subpopulations

African (AFR)

AF:

0.760

AC:

30662

AN:

40346

American (AMR)

AF:

0.855

AC:

12722

AN:

14880

Ashkenazi Jewish (ASJ)

AF:

0.775

AC:

2649

AN:

3420

East Asian (EAS)

AF:

0.937

AC:

4739

AN:

5058

South Asian (SAS)

AF:

0.849

AC:

3946

AN:

4650

European-Finnish (FIN)

AF:

0.792

AC:

7442

AN:

9400

Middle Eastern (MID)

AF:

0.731

AC:

212

AN:

290

European-Non Finnish (NFE)

AF:

0.849

AC:

56757

AN:

66830

Other (OTH)

AF:

0.801

AC:

1651

AN:

2062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

990

1980

2970

3960

4950

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

858

1716

2574

3432

4290

<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:

0.779

Hom.:

1612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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6-25708782-CTT-CTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over