chr17-9925187-C-CA

Position:

• chr17-9925187-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_201433.2(GAS7):​c.1138+288dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.42 (13201 hom., cov: 0)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.854

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-9925187-C-CA is Benign according to our data. Variant chr17-9925187-C-CA is described in ClinVar as [Benign]. Clinvar id is 1220653.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAS7	NM_201433.2	c.1138+288dupT		intron_variant		ENST00000432992.7	NP_958839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7	c.1138+288dupT		intron_variant		1	NM_201433.2	ENSP00000407552.2

Frequencies

GnomAD3 genomes AF: 0.416 AC: 62948 AN: 151330 Hom.: 13182 Cov.: 0

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.416 AC: 63016 AN: 151452 Hom.: 13201 Cov.: 0 AF XY: 0.412 AC XY: 30496 AN XY: 73982

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.382

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs11395653; hg19: chr17-9828504;