NM_201433.2:c.1318-173G>T

Variant names:

• chr17-9917514-C-A
• rs16958993
• NM_201433.2:c.1318-173G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_201433.2(GAS7):​c.1318-173G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0842 in 152,168 control chromosomes in the GnomAD database, including 1,091 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.084 (1091 hom., cov: 34)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.10
• 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 17-9917514-C-A is Benign according to our data. Variant chr17-9917514-C-A is described in ClinVar as Benign. ClinVar VariationId is 1295084.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 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.1318-173G>T		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1138-173G>T		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1126-173G>T		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.1318-173G>T		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1138-173G>T		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1138-173G>T		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12785 AN: 152050 Hom.: 1086 Cov.: 34

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0209

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0272

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0842 AC: 12815 AN: 152168 Hom.: 1091 Cov.: 34 AF XY: 0.0808 AC XY: 6008 AN XY: 74376

African (AFR) AF: 0.221 AC: 9168 AN: 41494

American (AMR) AF: 0.0439 AC: 672 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3472

East Asian (EAS) AF: 0.0209 AC: 108 AN: 5164

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4812

European-Finnish (FIN) AF: 0.0272 AC: 288 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0332 AC: 2260 AN: 68006

Other (OTH) AF: 0.0559 AC: 118 AN: 2112

Alfa AF: 0.0307 Hom.: 38

Bravo AF: 0.0903

Asia WGS AF: 0.0280 AC: 101 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.14
DANN	Benign	0.75
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs16958993; hg19: chr17-9820831;