17-9925431-CCTT-C

Variant summary

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

The NM_201433.2(GAS7):c.1138+42_1138+44del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,607,508 control chromosomes in the GnomAD database, including 13,790 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1493 hom., cov: 29)
  • Exomes 𝑓: 0.13 (12297 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.00900

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 -10 ACMG points.

• BP6: Variant 17-9925431-CCTT-C is Benign according to our data. Variant chr17-9925431-CCTT-C is described in ClinVar as [Benign]. Clinvar id is 1226902.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1138+42_1138+44del		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1138+42_1138+44del		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21175 AN: 152078 Hom.: 1490 Cov.: 29

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.146

GnomAD3 exomes AF: 0.141 AC: 35222 AN: 250158 Hom.: 2608 AF XY: 0.139 AC XY: 18755 AN XY: 135180

Gnomad AFR exome AF: 0.152

Gnomad AMR exome AF: 0.189

Gnomad ASJ exome AF: 0.199

Gnomad EAS exome AF: 0.0799

Gnomad SAS exome AF: 0.147

Gnomad FIN exome AF: 0.145

Gnomad NFE exome AF: 0.127

Gnomad OTH exome AF: 0.140

GnomAD4 exome AF: 0.127 AC: 184339 AN: 1455312 Hom.: 12297 AF XY: 0.127 AC XY: 91767 AN XY: 724306

Gnomad4 AFR exome AF: 0.149

Gnomad4 AMR exome AF: 0.188

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.0812

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.139

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.129

GnomAD4 genome AF: 0.139 AC: 21192 AN: 152196 Hom.: 1493 Cov.: 29 AF XY: 0.139 AC XY: 10306 AN XY: 74396

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0854

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.147

Alfa AF: 0.140 Hom.: 273

Bravo AF: 0.142

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

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: rs10615654; hg19: chr17-9828748;