rs9897528

chr17-10017066-G-Achr17-10017066-G-C

Variant summary

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

The NM_201433.2(GAS7):c.304+2711C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 149,912 control chromosomes in the GnomAD database, including 406 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 0.058 (406 hom., cov: 30)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.304+2711C>T		intron_variant		ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.304+2711C>T		intron_variant		1	NM_201433.2	P1

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8632 AN: 149810 Hom.: 398 Cov.: 30

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0297

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.00720

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0579 AC: 8673 AN: 149912 Hom.: 406 Cov.: 30 AF XY: 0.0566 AC XY: 4140 AN XY: 73208

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0296

Gnomad4 ASJ AF: 0.0263

Gnomad4 EAS AF: 0.0999

Gnomad4 SAS AF: 0.0654

Gnomad4 FIN AF: 0.00720

Gnomad4 NFE AF: 0.0287

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.0418 Hom.: 35

Bravo AF: 0.0618

Asia WGS AF: 0.108 AC: 373 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.68
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: rs9897528; hg19: chr17-9920383;