17-10102780-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAS7	NM_201433.2	c.184-82883G>A		intron_variant	Intron 1 of 13	ENST00000432992.7	NP_958839.1
GAS7	XM_011524044.4	c.-10+11662G>A		intron_variant	Intron 1 of 13		XP_011522346.1
GAS7	XM_047436954.1	c.-10+3075G>A		intron_variant	Intron 1 of 13		XP_047292910.1
GAS7	XM_047436955.1	c.-10+3409G>A		intron_variant	Intron 1 of 13		XP_047292911.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GAS7	ENST00000432992.7	c.184-82883G>A		intron_variant	Intron 1 of 13	1	NM_201433.2	ENSP00000407552.2
GAS7	ENST00000323816.8	c.-52+11662G>A		intron_variant	Intron 1 of 14	1		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

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.354

Alfa AF: 0.303 Hom.: 10137

Bravo AF: 0.387

Asia WGS AF: 0.280 AC: 972 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.49

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: rs16959323; hg19: chr17-10006097;