17-9913354-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201433.2(GAS7):c.*3874T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 232,094 control chromosomes in the GnomAD database, including 45,027 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 0.63 (31211 hom., cov: 32)
  • Exomes 𝑓: 0.58 (13816 hom.)
• Consequence: GAS7 NM_201433.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS7	NM_201433.2	c.*3874T>C		3_prime_UTR_variant	14/14	ENST00000432992.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS7	ENST00000432992.7	c.*3874T>C		3_prime_UTR_variant	14/14	1	NM_201433.2	P1
GAS7	ENST00000323816.8	c.*3874T>C		3_prime_UTR_variant	15/15	1
GAS7	ENST00000437099.6	c.*3874T>C		3_prime_UTR_variant	14/14	1

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96078 AN: 151982 Hom.: 31179 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.590

GnomAD4 exome AF: 0.583 AC: 46669 AN: 79994 Hom.: 13816 Cov.: 0 AF XY: 0.581 AC XY: 21406 AN XY: 36854

Gnomad4 AFR exome AF: 0.773

Gnomad4 AMR exome AF: 0.555

Gnomad4 ASJ exome AF: 0.452

Gnomad4 EAS exome AF: 0.579

Gnomad4 SAS exome AF: 0.450

Gnomad4 FIN exome AF: 0.559

Gnomad4 NFE exome AF: 0.588

Gnomad4 OTH exome AF: 0.576

GnomAD4 genome AF: 0.632 AC: 96157 AN: 152100 Hom.: 31211 Cov.: 32 AF XY: 0.625 AC XY: 46448 AN XY: 74366

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.586

Alfa AF: 0.594 Hom.: 36115

Bravo AF: 0.639

Asia WGS AF: 0.556 AC: 1937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.59
Dann	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2270121; hg19: chr17-9816671; COSMIC: COSV60433949; COSMIC: COSV60433949;