17-9917932-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.1317+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,105,584 control chromosomes in the GnomAD database, including 127,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.39 (13439 hom., cov: 34)
  • Exomes 𝑓: 0.48 (114521 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.77

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=-0.97).
• BP6: Variant 17-9917932-C-T is Benign according to our data. Variant chr17-9917932-C-T is described in ClinVar as [Benign]. Clinvar id is 1271504.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1317+69G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1317+69G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58892 AN: 152050 Hom.: 13442 Cov.: 34

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.484 AC: 461207 AN: 953414 Hom.: 114521 AF XY: 0.482 AC XY: 235242 AN XY: 488124

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.474

Gnomad4 ASJ exome AF: 0.434

Gnomad4 EAS exome AF: 0.420

Gnomad4 SAS exome AF: 0.399

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.515

Gnomad4 OTH exome AF: 0.460

GnomAD4 genome AF: 0.387 AC: 58889 AN: 152170 Hom.: 13439 Cov.: 34 AF XY: 0.384 AC XY: 28550 AN XY: 74380

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.388

Alfa AF: 0.465 Hom.: 3574

Bravo AF: 0.376

Asia WGS AF: 0.402 AC: 1395 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 18, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.011
Dann	Benign	0.70

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: rs11078822; hg19: chr17-9821249;