17-10117188-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201433.2(GAS7):c.183+81020G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,484 control chromosomes in the GnomAD database, including 15,986 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15986 hom., cov: 31)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.183+81020G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.183+81020G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68146 AN: 151366 Hom.: 15986 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.450 AC: 68165 AN: 151484 Hom.: 15986 Cov.: 31 AF XY: 0.457 AC XY: 33843 AN XY: 73974

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.477

Alfa AF: 0.488 Hom.: 22591

Bravo AF: 0.438

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.73

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: rs9897130; hg19: chr17-10020505;