17-9918135-C-T

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.1219-36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0377 in 1,495,646 control chromosomes in the GnomAD database, including 1,300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.034 (127 hom., cov: 33)
  • Exomes 𝑓: 0.038 (1173 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.96

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=-0.97).
• BP6: Variant 17-9918135-C-T is Benign according to our data. Variant chr17-9918135-C-T is described in ClinVar as [Benign]. Clinvar id is 1286767.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1219-36G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1219-36G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5192 AN: 152204 Hom.: 127 Cov.: 33

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0279

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0407

GnomAD3 exomes AF: 0.0380 AC: 9095 AN: 239542 Hom.: 245 AF XY: 0.0393 AC XY: 5092 AN XY: 129680

Gnomad AFR exome AF: 0.0105

Gnomad AMR exome AF: 0.0193

Gnomad ASJ exome AF: 0.0395

Gnomad EAS exome AF: 0.00203

Gnomad SAS exome AF: 0.0274

Gnomad FIN exome AF: 0.0987

Gnomad NFE exome AF: 0.0451

Gnomad OTH exome AF: 0.0467

GnomAD4 exome AF: 0.0381 AC: 51240 AN: 1343324 Hom.: 1173 Cov.: 20 AF XY: 0.0384 AC XY: 25857 AN XY: 673764

Gnomad4 AFR exome AF: 0.0120

Gnomad4 AMR exome AF: 0.0194

Gnomad4 ASJ exome AF: 0.0396

Gnomad4 EAS exome AF: 0.000998

Gnomad4 SAS exome AF: 0.0284

Gnomad4 FIN exome AF: 0.0936

Gnomad4 NFE exome AF: 0.0389

Gnomad4 OTH exome AF: 0.0409

GnomAD4 genome AF: 0.0341 AC: 5191 AN: 152322 Hom.: 127 Cov.: 33 AF XY: 0.0365 AC XY: 2722 AN XY: 74490

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0278

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0391 Hom.: 23

Bravo AF: 0.0284

Asia WGS AF: 0.0210 AC: 73 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

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.022
Dann	Benign	0.55

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: rs62064494; hg19: chr17-9821452;