17-9925199-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.1138+277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,880 control chromosomes in the GnomAD database, including 7,248 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.30 (7248 hom., cov: 31)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.61

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=-0.81).
• BP6: Variant 17-9925199-C-T is Benign according to our data. Variant chr17-9925199-C-T is described in ClinVar as [Benign]. Clinvar id is 1288305.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1138+277G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1138+277G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45949 AN: 151762 Hom.: 7227 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.268

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.303 AC: 46021 AN: 151880 Hom.: 7248 Cov.: 31 AF XY: 0.300 AC XY: 22232 AN XY: 74218

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.273

Alfa AF: 0.272 Hom.: 668

Bravo AF: 0.303

Asia WGS AF: 0.246 AC: 857 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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.22
Dann	Benign	0.48

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs12453300; hg19: chr17-9828516;