9-85552926-G-T

Position:

• chr9-85552926-G-T

Variant summary

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

The NM_001330701.2(AGTPBP1):​c.3504-5640C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,126 control chromosomes in the GnomAD database, including 8,939 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 0.28 (8939 hom., cov: 33)
• Consequence: AGTPBP1 NM_001330701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGTPBP1	NM_001330701.2	c.3504-5640C>A		intron_variant		ENST00000357081.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGTPBP1	ENST00000357081.8	c.3504-5640C>A		intron_variant		5	NM_001330701.2	P1
AGTPBP1	ENST00000376083.7	c.3384-5640C>A		intron_variant		1
AGTPBP1	ENST00000337006.8	c.3660-5640C>A		intron_variant		5
AGTPBP1	ENST00000628899.1	c.3540-5640C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42413 AN: 152008 Hom.: 8908 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.279 AC: 42497 AN: 152126 Hom.: 8939 Cov.: 33 AF XY: 0.279 AC XY: 20729 AN XY: 74378

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.236

Alfa AF: 0.153 Hom.: 947

Bravo AF: 0.295

Asia WGS AF: 0.358 AC: 1242 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.7
DANN	Benign	0.22

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

Publications

LitVar

Other links and lift over

dbSNP: rs10868320; hg19: chr9-88167841;