17-10117188-C-T

Variant names:

• chr17-10117188-C-T
• rs9897130
• NM_201433.2:c.183+81020G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GAS7	NM_201433.2	c.183+81020G>A		intron_variant	Intron 1 of 13	ENST00000432992.7	NP_958839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7	c.183+81020G>A		intron_variant	Intron 1 of 13	1	NM_201433.2	ENSP00000407552.2

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

African (AFR) AF: 0.343 AC: 14185 AN: 41396

American (AMR) AF: 0.441 AC: 6711 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1744 AN: 3462

East Asian (EAS) AF: 0.652 AC: 3335 AN: 5118

South Asian (SAS) AF: 0.462 AC: 2220 AN: 4802

European-Finnish (FIN) AF: 0.552 AC: 5769 AN: 10450

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32714 AN: 67746

Other (OTH) AF: 0.477 AC: 996 AN: 2088

Alfa AF: 0.477 Hom.: 28840

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
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9897130; hg19: chr17-10020505;