rs7930612

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024783.4(AGBL2):​c.2017-445G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,180 control chromosomes in the GnomAD database, including 1,203 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 0.12 ( 1203 hom., cov: 32)

Consequence

AGBL2
NM_024783.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.146
Variant links:
Genes affected
AGBL2 (HGNC:26296): (AGBL carboxypeptidase 2) Predicted to enable metallocarboxypeptidase activity. Predicted to be involved in protein side chain deglutamylation. Located in centriole and ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AGBL2NM_024783.4 linkuse as main transcriptc.2017-445G>T intron_variant ENST00000525123.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGBL2ENST00000525123.6 linkuse as main transcriptc.2017-445G>T intron_variant 1 NM_024783.4 P2Q5U5Z8-1
AGBL2ENST00000528609.5 linkuse as main transcriptc.*144-445G>T intron_variant, NMD_transcript_variant 1
AGBL2ENST00000528244.5 linkuse as main transcriptc.1903-445G>T intron_variant 2 A2
AGBL2ENST00000529712.5 linkuse as main transcriptn.2550+2127G>T intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.119
AC:
18136
AN:
152062
Hom.:
1202
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0871
Gnomad AMI
AF:
0.0462
Gnomad AMR
AF:
0.0989
Gnomad ASJ
AF:
0.170
Gnomad EAS
AF:
0.0411
Gnomad SAS
AF:
0.0573
Gnomad FIN
AF:
0.130
Gnomad MID
AF:
0.118
Gnomad NFE
AF:
0.150
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.119
AC:
18138
AN:
152180
Hom.:
1203
Cov.:
32
AF XY:
0.116
AC XY:
8648
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0871
Gnomad4 AMR
AF:
0.0987
Gnomad4 ASJ
AF:
0.170
Gnomad4 EAS
AF:
0.0410
Gnomad4 SAS
AF:
0.0574
Gnomad4 FIN
AF:
0.130
Gnomad4 NFE
AF:
0.150
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.142
Hom.:
2010
Bravo
AF:
0.117
Asia WGS
AF:
0.0630
AC:
219
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.5
DANN
Benign
0.50

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7930612; hg19: chr11-47699398; API