Genetic Variant ENSG00000290199:n.310-20658A>G (chr22-23947178-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000703580.1(ENSG00000290199):n.310-20658A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0000097 ( 0 hom., cov: 17)

Consequence

ENSG00000290199
ENST00000703580.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

7 publications found

Variant links:

Genes affected

ENSG00000290199 (HGNC:):

ENSG00000290199 links:

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new If you want to explore the variant's impact on the transcript ENST00000703580.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000703580.1. 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

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000290199	ENST00000703580.1	n.310-20658A>G	intron	N/A
ENSG00000290199	ENST00000717616.1	n.136-20658A>G	intron	N/A
ENSG00000290199	ENST00000717617.1	n.136-20658A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00000971

AC:

AN:

102998

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000209

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.00000971

AC:

AN:

102998

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

49106

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

28812

American (AMR)

AF:

0.00

AC:

AN:

9636

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2504

East Asian (EAS)

AF:

0.00

AC:

AN:

3776

South Asian (SAS)

AF:

0.00

AC:

AN:

2444

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5872

Middle Eastern (MID)

AF:

0.00

AC:

AN:

230

European-Non Finnish (NFE)

AF:

0.0000209

AC:

AN:

47876

Other (OTH)

AF:

0.00

AC:

AN:

1336

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.75

(source)

DANN

Benign

0.20

PhyloP100

-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over