rs7048878

Variant names:

• chr9-85783990-C-T
• rs7048878
• XM_047423086.1:c.-34+7497G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657430.1(ENSG00000230303):​n.3868G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,060 control chromosomes in the GnomAD database, including 12,687 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 (12687 hom., cov: 32)
• Consequence: ENSG00000230303 ENST00000657430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781
• Publications: 2 publications found

Genes affected

AGTPBP1 (HGNC:17258): (ATP/GTP binding carboxypeptidase 1) NNA1 is a zinc carboxypeptidase that contains nuclear localization signals and an ATP/GTP-binding motif that was initially cloned from regenerating spinal cord neurons of the mouse.[supplied by OMIM, Jul 2002]

AGTPBP1 Gene-Disease associations (from GenCC):

• neurodegeneration, childhood-onset, with cerebellar atrophy

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
• pontocerebellar hypoplasia type 1

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000230303 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657430.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230303	ENST00000657430.1		n.3868G>A		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000230303	ENST00000665432.1		n.3739G>A		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000234424	ENST00000422653.1	TSL:6	n.1076-2114C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58044 AN: 151942 Hom.: 12659 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.382 AC: 58125 AN: 152060 Hom.: 12687 Cov.: 32 AF XY: 0.390 AC XY: 28973 AN XY: 74330

African (AFR) AF: 0.586 AC: 24315 AN: 41484

American (AMR) AF: 0.425 AC: 6500 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1744 AN: 5174

South Asian (SAS) AF: 0.490 AC: 2360 AN: 4818

European-Finnish (FIN) AF: 0.362 AC: 3820 AN: 10560

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17180 AN: 67960

Other (OTH) AF: 0.364 AC: 768 AN: 2108

Alfa AF: 0.333 Hom.: 1570

Bravo AF: 0.395

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.59
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs7048878; hg19: chr9-88398905;