chr17-9919441-T-C

Variant names:

• chr17-9919441-T-C
• rs9897353
• NM_201433.2:c.1218+185A>G

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.1218+185A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0878 in 152,078 control chromosomes in the GnomAD database, including 1,734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.088 (1734 hom., cov: 32)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.16
• Publications: 0 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=-0.86).
• BP6: Variant 17-9919441-T-C is Benign according to our data. Variant chr17-9919441-T-C is described in ClinVar as Benign. ClinVar VariationId is 1249262.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 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.1218+185A>G		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1038+185A>G		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1026+185A>G		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.1218+185A>G		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1038+185A>G		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1038+185A>G		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13310 AN: 151960 Hom.: 1727 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00201

Gnomad OTH AF: 0.0709

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

GnomAD4 genome AF: 0.0878 AC: 13349 AN: 152078 Hom.: 1734 Cov.: 32 AF XY: 0.0861 AC XY: 6404 AN XY: 74348

African (AFR) AF: 0.281 AC: 11632 AN: 41412

American (AMR) AF: 0.0351 AC: 537 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00779 AC: 27 AN: 3464

East Asian (EAS) AF: 0.0943 AC: 486 AN: 5152

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4822

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00201 AC: 137 AN: 68010

Other (OTH) AF: 0.0697 AC: 147 AN: 2110

Alfa AF: 0.0317 Hom.: 923

Bravo AF: 0.0975

Asia WGS AF: 0.0810 AC: 280 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	-0.86
CADD	Benign	0.32
DANN	Benign	0.34
PhyloP100		-1.2
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: rs9897353; hg19: chr17-9822758;