rs9895531

Positions:

• chr17-10147354-G-A
• chr17-10147354-G-T

Variant summary

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

The ENST00000432992.7(GAS7):​c.183+50854C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 152,042 control chromosomes in the GnomAD database, including 15,252 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 (15252 hom., cov: 33)
• Consequence: GAS7 ENST00000432992.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GAS7	NM_201433.2	c.183+50854C>T		intron_variant		ENST00000432992.7	NP_958839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7	c.183+50854C>T		intron_variant		1	NM_201433.2	ENSP00000407552	P1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67092 AN: 151924 Hom.: 15252 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.441 AC: 67108 AN: 152042 Hom.: 15252 Cov.: 33 AF XY: 0.442 AC XY: 32841 AN XY: 74326

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.468

Alfa AF: 0.455 Hom.: 2359

Bravo AF: 0.439

Asia WGS AF: 0.526 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.017
DANN	Benign	0.58

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: rs9895531; hg19: chr17-10050671;