17-10147354-G-A

Variant names:

• chr17-10147354-G-A
• rs9895531
• NM_201433.2:c.183+50854C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201433.2(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 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GAS7	NM_201433.2	c.183+50854C>T		intron_variant	Intron 1 of 13	ENST00000432992.7	NP_958839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7	c.183+50854C>T		intron_variant	Intron 1 of 13	1	NM_201433.2	ENSP00000407552.2

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

African (AFR) AF: 0.353 AC: 14648 AN: 41468

American (AMR) AF: 0.448 AC: 6844 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2194 AN: 3468

East Asian (EAS) AF: 0.642 AC: 3321 AN: 5174

South Asian (SAS) AF: 0.494 AC: 2384 AN: 4824

European-Finnish (FIN) AF: 0.425 AC: 4484 AN: 10562

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31628 AN: 67974

Other (OTH) AF: 0.468 AC: 986 AN: 2108

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
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9895531; hg19: chr17-10050671;