chr17-9971888-T-C

Variant names:

• chr17-9971888-T-C
• rs3786094
• NM_201433.2:c.386-2126A>G

Variant summary

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

The NM_201433.2(GAS7):​c.386-2126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,910 control chromosomes in the GnomAD database, including 15,133 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 0.44 (15133 hom., cov: 32)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 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.386-2126A>G		intron	N/A	NP_958839.1
	GAS7	NM_201432.2		c.206-2126A>G		intron	N/A	NP_958836.1
	GAS7	NM_001130831.2		c.194-2126A>G		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.386-2126A>G		intron	N/A	ENSP00000407552.2
	GAS7	ENST00000323816.8	TSL:1	c.206-2126A>G		intron	N/A	ENSP00000322608.5
	GAS7	ENST00000585266.5	TSL:1	c.206-2126A>G		intron	N/A	ENSP00000464240.2

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67051 AN: 151792 Hom.: 15131 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.442 AC: 67076 AN: 151910 Hom.: 15133 Cov.: 32 AF XY: 0.445 AC XY: 33050 AN XY: 74242

African (AFR) AF: 0.348 AC: 14405 AN: 41444

American (AMR) AF: 0.409 AC: 6256 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3470

East Asian (EAS) AF: 0.480 AC: 2473 AN: 5156

South Asian (SAS) AF: 0.498 AC: 2400 AN: 4818

European-Finnish (FIN) AF: 0.559 AC: 5893 AN: 10540

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.478 AC: 32439 AN: 67894

Other (OTH) AF: 0.464 AC: 977 AN: 2104

Alfa AF: 0.466 Hom.: 65905

Bravo AF: 0.429

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.44
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3786094; hg19: chr17-9875205;