17-9917566-C-T

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.1318-225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,312 control chromosomes in the GnomAD database, including 291 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.051 (291 hom., cov: 34)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.983

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=-0.85).
• BP6: Variant 17-9917566-C-T is Benign according to our data. Variant chr17-9917566-C-T is described in ClinVar as [Benign]. Clinvar id is 1266608.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1318-225G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1318-225G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7728 AN: 152194 Hom.: 287 Cov.: 34

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0509 AC: 7752 AN: 152312 Hom.: 291 Cov.: 34 AF XY: 0.0486 AC XY: 3619 AN XY: 74478

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0306

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0275

Gnomad4 NFE AF: 0.0330

Gnomad4 OTH AF: 0.0374

Alfa AF: 0.0417 Hom.: 41

Bravo AF: 0.0530

Asia WGS AF: 0.0220 AC: 78 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 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.1
Dann	Benign	0.82

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: rs59994052; hg19: chr17-9820883;