NM_201433.2:c.1318-225G>A

Variant names:

• chr17-9917566-C-T
• rs59994052
• NM_201433.2:c.1318-225G>A

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.1318-225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,312 control chromosomes in the GnomAD database, including 291 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.051 (291 hom., cov: 34)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.983
• 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=-0.85).
• BP6: Variant 17-9917566-C-T is Benign according to our data. Variant chr17-9917566-C-T is described in ClinVar as Benign. ClinVar VariationId is 1266608.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.103 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.1318-225G>A		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1138-225G>A		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1126-225G>A		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.1318-225G>A		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1138-225G>A		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1138-225G>A		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes AF: 0.0508 AC: 7728 AN: 152194 Hom.: 287 Cov.: 34

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0307

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0275

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0330

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0509 AC: 7752 AN: 152312 Hom.: 291 Cov.: 34 AF XY: 0.0486 AC XY: 3619 AN XY: 74478

African (AFR) AF: 0.105 AC: 4369 AN: 41560

American (AMR) AF: 0.0306 AC: 469 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5172

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4826

European-Finnish (FIN) AF: 0.0275 AC: 292 AN: 10626

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0330 AC: 2242 AN: 68034

Other (OTH) AF: 0.0374 AC: 79 AN: 2114

Alfa AF: 0.0419 Hom.: 282

Bravo AF: 0.0530

Asia WGS AF: 0.0220 AC: 78 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	-0.85
CADD	Benign	2.1
DANN	Benign	0.82
PhyloP100		-0.98
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: rs59994052; hg19: chr17-9820883;