17-9918157-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.1219-58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 1,253,650 control chromosomes in the GnomAD database, including 16,795 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.21 (4167 hom., cov: 33)
  • Exomes 𝑓: 0.14 (12628 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.12

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 17-9918157-C-T is Benign according to our data. Variant chr17-9918157-C-T is described in ClinVar as [Benign]. Clinvar id is 1228161.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1219-58G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1219-58G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31591 AN: 151940 Hom.: 4157 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.192

GnomAD4 exome AF: 0.137 AC: 150624 AN: 1101594 Hom.: 12628 AF XY: 0.138 AC XY: 77332 AN XY: 561200

Gnomad4 AFR exome AF: 0.363

Gnomad4 AMR exome AF: 0.248

Gnomad4 ASJ exome AF: 0.157

Gnomad4 EAS exome AF: 0.303

Gnomad4 SAS exome AF: 0.196

Gnomad4 FIN exome AF: 0.192

Gnomad4 NFE exome AF: 0.105

Gnomad4 OTH exome AF: 0.158

GnomAD4 genome AF: 0.208 AC: 31645 AN: 152056 Hom.: 4167 Cov.: 33 AF XY: 0.211 AC XY: 15683 AN XY: 74322

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.196

Alfa AF: 0.169 Hom.: 360

Bravo AF: 0.218

Asia WGS AF: 0.262 AC: 910 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.23
Dann	Benign	0.78

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: rs2270122; hg19: chr17-9821474; COSMIC: COSV60437971;