17-9917422-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_201433.2(GAS7):c.1318-81T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 989,216 control chromosomes in the GnomAD database, including 130,241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.48 (17817 hom., cov: 34)
  • Exomes 𝑓: 0.51 (112424 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.44

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

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 17-9917422-A-G is Benign according to our data. Variant chr17-9917422-A-G is described in ClinVar as [Benign]. Clinvar id is 1273039.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1318-81T>C		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1318-81T>C		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72713 AN: 152010 Hom.: 17801 Cov.: 34

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.471

GnomAD4 exome AF: 0.515 AC: 430805 AN: 837088 Hom.: 112424 AF XY: 0.512 AC XY: 223836 AN XY: 437508

Gnomad4 AFR exome AF: 0.402

Gnomad4 AMR exome AF: 0.453

Gnomad4 ASJ exome AF: 0.484

Gnomad4 EAS exome AF: 0.403

Gnomad4 SAS exome AF: 0.425

Gnomad4 FIN exome AF: 0.445

Gnomad4 NFE exome AF: 0.550

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.478 AC: 72770 AN: 152128 Hom.: 17817 Cov.: 34 AF XY: 0.471 AC XY: 35047 AN XY: 74350

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.468

Alfa AF: 0.525 Hom.: 27801

Bravo AF: 0.474

Asia WGS AF: 0.396 AC: 1378 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.098
Dann	Benign	0.17

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

Publications

LitVar

Other links and lift over

dbSNP: rs11078821; hg19: chr17-9820739; COSMIC: COSV60439555;