chr17-9917932-C-T

Variant names:

• chr17-9917932-C-T
• rs11078822
• NM_201433.2:c.1317+69G>A

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.1317+69G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,105,584 control chromosomes in the GnomAD database, including 127,960 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.39 (13439 hom., cov: 34)
  • Exomes 𝑓: 0.48 (114521 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.77
• Publications: 4 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=-0.97).
• BP6: Variant 17-9917932-C-T is Benign according to our data. Variant chr17-9917932-C-T is described in ClinVar as Benign. ClinVar VariationId is 1271504.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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+69G>A		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1137+69G>A		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1125+69G>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.1317+69G>A		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1137+69G>A		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1137+69G>A		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58892 AN: 152050 Hom.: 13442 Cov.: 34

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.484 AC: 461207 AN: 953414 Hom.: 114521 AF XY: 0.482 AC XY: 235242 AN XY: 488124

African (AFR) AF: 0.122 AC: 2884 AN: 23572

American (AMR) AF: 0.474 AC: 17025 AN: 35934

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 9023 AN: 20798

East Asian (EAS) AF: 0.420 AC: 15214 AN: 36226

South Asian (SAS) AF: 0.399 AC: 27817 AN: 69692

European-Finnish (FIN) AF: 0.444 AC: 20041 AN: 45182

Middle Eastern (MID) AF: 0.436 AC: 1421 AN: 3262

European-Non Finnish (NFE) AF: 0.515 AC: 348015 AN: 675748

Other (OTH) AF: 0.460 AC: 19767 AN: 43000

GnomAD4 genome AF: 0.387 AC: 58889 AN: 152170 Hom.: 13439 Cov.: 34 AF XY: 0.384 AC XY: 28550 AN XY: 74380

African (AFR) AF: 0.133 AC: 5536 AN: 41546

American (AMR) AF: 0.435 AC: 6659 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1543 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2268 AN: 5156

South Asian (SAS) AF: 0.395 AC: 1905 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4635 AN: 10588

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.514 AC: 34964 AN: 67964

Other (OTH) AF: 0.388 AC: 820 AN: 2114

Alfa AF: 0.465 Hom.: 3574

Bravo AF: 0.376

Asia WGS AF: 0.402 AC: 1395 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	-0.97
CADD	Benign	0.011
DANN	Benign	0.70
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: rs11078822; hg19: chr17-9821249;