17-10017066-G-A

Variant names:

• chr17-10017066-G-A
• rs9897528
• NM_201433.2:c.304+2711C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201433.2(GAS7):​c.304+2711C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 149,912 control chromosomes in the GnomAD database, including 406 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 0.058 (406 hom., cov: 30)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201433.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	NM_201433.2	MANE Select	c.304+2711C>T		intron	N/A	NP_958839.1
	GAS7	NM_201432.2		c.124+2711C>T		intron	N/A	NP_958836.1
	GAS7	NM_001130831.2		c.112+2711C>T		intron	N/A	NP_001124303.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	ENST00000432992.7	TSL:1 MANE Select	c.304+2711C>T		intron	N/A	ENSP00000407552.2
	GAS7	ENST00000323816.8	TSL:1	c.124+2711C>T		intron	N/A	ENSP00000322608.5
	GAS7	ENST00000585266.5	TSL:1	c.124+2711C>T		intron	N/A	ENSP00000464240.2

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8632 AN: 149810 Hom.: 398 Cov.: 30

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.00720

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0579 AC: 8673 AN: 149912 Hom.: 406 Cov.: 30 AF XY: 0.0566 AC XY: 4140 AN XY: 73208

African (AFR) AF: 0.126 AC: 5173 AN: 41006

American (AMR) AF: 0.0296 AC: 445 AN: 15024

Ashkenazi Jewish (ASJ) AF: 0.0263 AC: 91 AN: 3464

East Asian (EAS) AF: 0.0999 AC: 512 AN: 5126

South Asian (SAS) AF: 0.0654 AC: 310 AN: 4740

European-Finnish (FIN) AF: 0.00720 AC: 70 AN: 9718

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.0287 AC: 1941 AN: 67558

Other (OTH) AF: 0.0554 AC: 115 AN: 2074

Alfa AF: 0.0418 Hom.: 35

Bravo AF: 0.0618

Asia WGS AF: 0.108 AC: 373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.68
DANN	Benign	0.55
PhyloP100		-0.58
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: rs9897528; hg19: chr17-9920383;