chr17-9956782-A-G

Variant names:

• chr17-9956782-A-G
• rs11651517
• NM_201433.2:c.525+2420T>C

Variant summary

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

The NM_201433.2(GAS7):​c.525+2420T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,038 control chromosomes in the GnomAD database, including 18,129 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 0.48 (18129 hom., cov: 32)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAS7	NM_201433.2	c.525+2420T>C		intron_variant	Intron 5 of 13	ENST00000432992.7	NP_958839.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7	c.525+2420T>C		intron_variant	Intron 5 of 13	1	NM_201433.2	ENSP00000407552.2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72240 AN: 151920 Hom.: 18128 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.475 AC: 72262 AN: 152038 Hom.: 18129 Cov.: 32 AF XY: 0.477 AC XY: 35448 AN XY: 74322

African (AFR) AF: 0.306 AC: 12687 AN: 41452

American (AMR) AF: 0.478 AC: 7311 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1765 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1911 AN: 5160

South Asian (SAS) AF: 0.478 AC: 2307 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 6015 AN: 10568

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38534 AN: 67966

Other (OTH) AF: 0.497 AC: 1050 AN: 2112

Alfa AF: 0.490 Hom.: 3953

Bravo AF: 0.462

Asia WGS AF: 0.461 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.53
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: rs11651517; hg19: chr17-9860099;