17-9926569-G-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.1014+72C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,526,210 control chromosomes in the GnomAD database, including 13,467 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1529 hom., cov: 32)
  • Exomes 𝑓: 0.13 (11938 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.316

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=-0.77).
• BP6: Variant 17-9926569-G-T is Benign according to our data. Variant chr17-9926569-G-T is described in ClinVar as [Benign]. Clinvar id is 1228795.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.1014+72C>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1014+72C>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21344 AN: 152088 Hom.: 1526 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0850

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.128 AC: 176511 AN: 1374004 Hom.: 11938 AF XY: 0.128 AC XY: 88280 AN XY: 687088

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.189

Gnomad4 ASJ exome AF: 0.198

Gnomad4 EAS exome AF: 0.0814

Gnomad4 SAS exome AF: 0.143

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.130

GnomAD4 genome AF: 0.140 AC: 21361 AN: 152206 Hom.: 1529 Cov.: 32 AF XY: 0.140 AC XY: 10393 AN XY: 74412

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.0850

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0894 Hom.: 161

Bravo AF: 0.143

Asia WGS AF: 0.139 AC: 485 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	-0.77
Cadd	Benign	2.5
Dann	Benign	0.85

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: rs7216815; hg19: chr17-9829886; COSMIC: COSV60432770; COSMIC: COSV60432770;