17-10102780-C-T

Variant names:

• chr17-10102780-C-T
• rs16959323
• NM_201433.2:c.184-82883G>A

Variant summary

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

The NM_201433.2(GAS7):​c.184-82883G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 150,480 control chromosomes in the GnomAD database, including 13,023 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 0.38 (13023 hom., cov: 29)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201433.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	NM_201433.2	MANE Select	c.184-82883G>A		intron	N/A	NP_958839.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	ENST00000432992.7	TSL:1 MANE Select	c.184-82883G>A		intron	N/A	ENSP00000407552.2
	GAS7	ENST00000323816.8	TSL:1	c.-52+11662G>A		intron	N/A	ENSP00000322608.5

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57538 AN: 150370 Hom.: 12992 Cov.: 29

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.383 AC: 57618 AN: 150480 Hom.: 13023 Cov.: 29 AF XY: 0.381 AC XY: 27987 AN XY: 73362

African (AFR) AF: 0.645 AC: 26422 AN: 40964

American (AMR) AF: 0.266 AC: 4020 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 987 AN: 3454

East Asian (EAS) AF: 0.191 AC: 979 AN: 5126

South Asian (SAS) AF: 0.307 AC: 1463 AN: 4772

European-Finnish (FIN) AF: 0.342 AC: 3445 AN: 10068

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19170 AN: 67650

Other (OTH) AF: 0.354 AC: 744 AN: 2100

Alfa AF: 0.313 Hom.: 15423

Bravo AF: 0.387

Asia WGS AF: 0.280 AC: 972 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.49
PhyloP100		0.069
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: rs16959323; hg19: chr17-10006097;