chr17-10127773-C-T

Variant names:

• chr17-10127773-C-T
• rs12150284
• NM_201433.2:c.183+70435G>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.183+70435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,900 control chromosomes in the GnomAD database, including 8,266 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 0.31 (8266 hom., cov: 32)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995
• Publications: 29 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GAS7	NM_201433.2	c.183+70435G>A		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+70435G>A		intron_variant	Intron 1 of 13	1	NM_201433.2	ENSP00000407552.2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47435 AN: 151782 Hom.: 8266 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.312 AC: 47445 AN: 151900 Hom.: 8266 Cov.: 32 AF XY: 0.315 AC XY: 23411 AN XY: 74242

African (AFR) AF: 0.178 AC: 7380 AN: 41440

American (AMR) AF: 0.323 AC: 4923 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1108 AN: 3464

East Asian (EAS) AF: 0.510 AC: 2614 AN: 5128

South Asian (SAS) AF: 0.268 AC: 1293 AN: 4818

European-Finnish (FIN) AF: 0.382 AC: 4020 AN: 10526

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24936 AN: 67956

Other (OTH) AF: 0.352 AC: 742 AN: 2108

Alfa AF: 0.350 Hom.: 38896

Bravo AF: 0.305

Asia WGS AF: 0.332 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.45
PhyloP100		0.99
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: rs12150284; hg19: chr17-10031090; COSMIC: COSV71564148;