rs7048878

Variant names:

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

Variant summary

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

The XM_047423086.1(AGTPBP1):​c.-34+7497G>A variant causes a intron 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: AGTPBP1 XM_047423086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

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]

ENSG00000230303 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGTPBP1	XM_047423086.1	c.-34+7497G>A		intron_variant	Intron 4 of 28		XP_047279042.1
AGTPBP1	XM_047423087.1	c.-34+7497G>A		intron_variant	Intron 3 of 27		XP_047279043.1
AGTPBP1	XM_047423088.1	c.-34+7497G>A		intron_variant	Intron 5 of 29		XP_047279044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230303	ENST00000657430.1	n.3868G>A		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000230303	ENST00000665432.1	n.3739G>A		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000234424	ENST00000422653.1	n.1076-2114C>T		intron_variant	Intron 6 of 6	6

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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.364

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7048878; hg19: chr9-88398905;