17-9917378-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.1318-37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 1,427,730 control chromosomes in the GnomAD database, including 217,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.52 (20843 hom., cov: 35)
  • Exomes 𝑓: 0.55 (196343 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.495

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=-0.9).
• BP6: Variant 17-9917378-C-T is Benign according to our data. Variant chr17-9917378-C-T is described in ClinVar as [Benign]. Clinvar id is 1222796.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.1318-37G>A		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.1318-37G>A		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78978 AN: 152046 Hom.: 20835 Cov.: 35

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.516

GnomAD3 exomes AF: 0.526 AC: 130736 AN: 248758 Hom.: 34802 AF XY: 0.521 AC XY: 70145 AN XY: 134526

Gnomad AFR exome AF: 0.451

Gnomad AMR exome AF: 0.492

Gnomad ASJ exome AF: 0.507

Gnomad EAS exome AF: 0.576

Gnomad SAS exome AF: 0.408

Gnomad FIN exome AF: 0.568

Gnomad NFE exome AF: 0.563

Gnomad OTH exome AF: 0.541

GnomAD4 exome AF: 0.551 AC: 702486 AN: 1275566 Hom.: 196343 Cov.: 19 AF XY: 0.546 AC XY: 351749 AN XY: 644410

Gnomad4 AFR exome AF: 0.436

Gnomad4 AMR exome AF: 0.493

Gnomad4 ASJ exome AF: 0.501

Gnomad4 EAS exome AF: 0.559

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.559

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.536

GnomAD4 genome AF: 0.519 AC: 79016 AN: 152164 Hom.: 20843 Cov.: 35 AF XY: 0.517 AC XY: 38434 AN XY: 74376

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.513

Alfa AF: 0.554 Hom.: 51766

Bravo AF: 0.511

Asia WGS AF: 0.479 AC: 1666 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 18, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.062
Dann	Benign	0.66

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: rs4791910; hg19: chr17-9820695;