Variant 17-9918297-G-GA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_201433.2(GAS7):c.1219-199dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.84 ( 53757 hom., cov: 0)

Consequence

GAS7
NM_201433.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.412

Variant links:

Genes affected

GAS7 (HGNC:4169): (growth arrest specific 7) Growth arrest-specific 7 is expressed primarily in terminally differentiated brain cells and predominantly in mature cerebellar Purkinje neurons. GAS7 plays a putative role in neuronal development. Several transcript variants encoding proteins which vary in the N-terminus have been described. [provided by RefSeq, Jul 2008]

GAS7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 17-9918297-G-GA is Benign according to our data. Variant chr17-9918297-G-GA is described in ClinVar as [Benign]. Clinvar id is 1178676.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAS7	NM_201433.2 link	c.1219-199dupT		intron_variant		ENST00000432992.7	NP_958839.1	O60861-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7 link	c.1219-199_1219-198insT		intron_variant		1	NM_201433.2	ENSP00000407552.2		O60861-3

Frequencies

GnomAD3 genomes

AF:

0.840

AC:

127346

AN:

151688

Hom.:

53699

Cov.:

show subpopulations

Gnomad AFR

AF:

0.919

Gnomad AMI

AF:

0.835

Gnomad AMR

AF:

0.810

Gnomad ASJ

AF:

0.811

Gnomad EAS

AF:

0.853

Gnomad SAS

AF:

0.796

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.863

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.825

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

GnomAD4 genome

AF:

0.840

AC:

127461

AN:

151808

Hom.:

53757

Cov.:

AF XY:

0.837

AC XY:

62072

AN XY:

74176

show subpopulations

Gnomad4 AFR

AF:

0.920

Gnomad4 AMR

AF:

0.810

Gnomad4 ASJ

AF:

0.811

Gnomad4 EAS

AF:

0.853

Gnomad4 SAS

AF:

0.794

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.827

Alfa

AF:

0.832

Hom.:

5650

Bravo

AF:

0.843

Asia WGS

AF:

0.841

AC:

2926

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over