17-9917436-G-C

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.1318-95C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 870,906 control chromosomes in the GnomAD database, including 1,502 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.063 (957 hom., cov: 34)
  • Exomes 𝑓: 0.010 (545 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.638

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=-0.87).
• BP6: Variant 17-9917436-G-C is Benign according to our data. Variant chr17-9917436-G-C is described in ClinVar as [Benign]. Clinvar id is 1270921.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1318-95C>G		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1318-95C>G		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.0626 AC: 9522 AN: 152204 Hom.: 948 Cov.: 34

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00113

Gnomad OTH AF: 0.0392

GnomAD4 exome AF: 0.0104 AC: 7487 AN: 718584 Hom.: 545 AF XY: 0.00909 AC XY: 3438 AN XY: 378182

Gnomad4 AFR exome AF: 0.220

Gnomad4 AMR exome AF: 0.0191

Gnomad4 ASJ exome AF: 0.00573

Gnomad4 EAS exome AF: 0.0271

Gnomad4 SAS exome AF: 0.00532

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000862

Gnomad4 OTH exome AF: 0.0201

GnomAD4 genome AF: 0.0628 AC: 9566 AN: 152322 Hom.: 957 Cov.: 34 AF XY: 0.0610 AC XY: 4545 AN XY: 74478

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.0289

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.0209

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00113

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0486 Hom.: 58

Bravo AF: 0.0714

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	-0.87
Cadd	Benign	1.4
Dann	Benign	0.81

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: rs57391370; hg19: chr17-9820753;