rs2270121

Variant names:

• chr17-9913354-A-C
• rs2270121
• NM_201433.2:c.*3874T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-9913354-A-C
• chr17-9913354-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_201433.2(GAS7):​c.*3874T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 80,132 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: GAS7 NM_201433.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 22 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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.*3874T>G		3_prime_UTR	Exon 14 of 14	NP_958839.1
	GAS7	NM_201432.2		c.*3874T>G		3_prime_UTR	Exon 14 of 14	NP_958836.1
	GAS7	NM_001130831.2		c.*3874T>G		3_prime_UTR	Exon 14 of 14	NP_001124303.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	ENST00000432992.7	TSL:1 MANE Select	c.*3874T>G		3_prime_UTR	Exon 14 of 14	ENSP00000407552.2
	GAS7	ENST00000323816.8	TSL:1	c.*3874T>G		3_prime_UTR	Exon 15 of 15	ENSP00000322608.5
	GAS7	ENST00000437099.6	TSL:1	c.*3874T>G		3_prime_UTR	Exon 14 of 14	ENSP00000410108.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.0000125 AC: 1 AN: 80132 Hom.: 0 Cov.: 0 AF XY: 0.0000271 AC XY: 1 AN XY: 36918

African (AFR) AF: 0.00 AC: 0 AN: 3828

American (AMR) AF: 0.00 AC: 0 AN: 2462

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5046

East Asian (EAS) AF: 0.00 AC: 0 AN: 11278

South Asian (SAS) AF: 0.00 AC: 0 AN: 694

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 476

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 478

European-Non Finnish (NFE) AF: 0.0000203 AC: 1 AN: 49214

Other (OTH) AF: 0.00 AC: 0 AN: 6656

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.56
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2270121; hg19: chr17-9816671;