rs11078822

Variant names:

• chr17-9917932-C-A
• rs11078822
• NM_201433.2:c.1317+69G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-9917932-C-A
• chr17-9917932-C-T

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.1317+69G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000314 in 955,718 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: 34)
  • Exomes 𝑓: 0.0000031 (0 hom.)
• Consequence: GAS7 NM_201433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 0 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=-0.93).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	NM_201433.2	MANE Select	c.1317+69G>T		intron	N/A	NP_958839.1	O60861-3
	GAS7	NM_201432.2		c.1137+69G>T		intron	N/A	NP_958836.1	O60861-4
	GAS7	NM_001130831.2		c.1125+69G>T		intron	N/A	NP_001124303.1	O60861-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS7	ENST00000432992.7	TSL:1 MANE Select	c.1317+69G>T		intron	N/A	ENSP00000407552.2	O60861-3
	GAS7	ENST00000323816.8	TSL:1	c.1137+69G>T		intron	N/A	ENSP00000322608.5	O60861-4
	GAS7	ENST00000585266.5	TSL:1	c.1137+69G>T		intron	N/A	ENSP00000464240.2	O60861-4

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000314 AC: 3 AN: 955718 Hom.: 0 AF XY: 0.00000204 AC XY: 1 AN XY: 489250

African (AFR) AF: 0.00 AC: 0 AN: 23610

American (AMR) AF: 0.00 AC: 0 AN: 36006

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20824

East Asian (EAS) AF: 0.00 AC: 0 AN: 36272

South Asian (SAS) AF: 0.00 AC: 0 AN: 69796

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45252

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3266

European-Non Finnish (NFE) AF: 0.00000443 AC: 3 AN: 677596

Other (OTH) AF: 0.00 AC: 0 AN: 43096

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0050
DANN	Benign	0.61
PhyloP100		-1.8

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: rs11078822; hg19: chr17-9821249;