17-9917806-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_201433.2(GAS7):c.1317+195G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,080 control chromosomes in the GnomAD database, including 17,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17590 hom., cov: 33)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.85

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-9917806-C-G is Benign according to our data. Variant chr17-9917806-C-G is described in ClinVar as [Benign]. Clinvar id is 1178248.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1317+195G>C		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1317+195G>C		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72898 AN: 151962 Hom.: 17588 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72932 AN: 152080 Hom.: 17590 Cov.: 33 AF XY: 0.472 AC XY: 35102 AN XY: 74342

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.449

Alfa AF: 0.502 Hom.: 2345

Bravo AF: 0.485

Asia WGS AF: 0.460 AC: 1600 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

Nov 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.0080
Dann	Benign	0.49

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

Other links and lift over

dbSNP: rs9908886; hg19: chr17-9821123;