rs3786094

Positions:

• chr17-9971888-T-C
• chr17-9971888-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201433.2(GAS7):​c.386-2126A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,910 control chromosomes in the GnomAD database, including 15,133 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (15133 hom., cov: 32)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.386-2126A>G		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.386-2126A>G		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67051 AN: 151792 Hom.: 15131 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.442 AC: 67076 AN: 151910 Hom.: 15133 Cov.: 32 AF XY: 0.445 AC XY: 33050 AN XY: 74242

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.464

Alfa AF: 0.471 Hom.: 28552

Bravo AF: 0.429

Asia WGS AF: 0.492 AC: 1712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs3786094; hg19: chr17-9875205;