rs11656696

Positions:

• chr17-10130362-C-A
• chr17-10130362-C-G

Variant summary

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

The NM_201433.2(GAS7):​c.183+67846G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 149,672 control chromosomes in the GnomAD database, including 10,393 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 0.36 (10393 hom., cov: 29)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.183+67846G>T		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.183+67846G>T		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.360 AC: 53816 AN: 149584 Hom.: 10389 Cov.: 29

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.360 AC: 53828 AN: 149672 Hom.: 10393 Cov.: 29 AF XY: 0.361 AC XY: 26288 AN XY: 72870

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.386

Alfa AF: 0.390 Hom.: 7950

Bravo AF: 0.351

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.50

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: rs11656696; hg19: chr17-10033679;