chr17-9917806-C-G

Variant names:

• chr17-9917806-C-G
• rs9908886
• NM_201433.2:c.1317+195G>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_201433.2(GAS7):​c.1317+195G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,080 control chromosomes in the GnomAD database, including 17,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.48 (17590 hom., cov: 33)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.85
• 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-9917806-C-G is Benign according to our data. Variant chr17-9917806-C-G is described in ClinVar as Benign. ClinVar VariationId is 1178248.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	NM_201433.2	MANE Select	c.1317+195G>C		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1137+195G>C		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1125+195G>C		intron	N/A	NP_001124303.1	O60861-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	ENST00000432992.7	TSL:1 MANE Select	c.1317+195G>C		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1137+195G>C		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1137+195G>C		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72898 AN: 151962 Hom.: 17588 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72932 AN: 152080 Hom.: 17590 Cov.: 33 AF XY: 0.472 AC XY: 35102 AN XY: 74342

African (AFR) AF: 0.478 AC: 19823 AN: 41470

American (AMR) AF: 0.467 AC: 7142 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3470

East Asian (EAS) AF: 0.518 AC: 2677 AN: 5166

South Asian (SAS) AF: 0.411 AC: 1982 AN: 4822

European-Finnish (FIN) AF: 0.400 AC: 4235 AN: 10586

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34121 AN: 67964

Other (OTH) AF: 0.449 AC: 945 AN: 2106

Alfa AF: 0.502 Hom.: 2345

Bravo AF: 0.485

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.49
PhyloP100		-1.8
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: rs9908886; hg19: chr17-9821123;