chr1-48742946-G-C

Variant names:

• chr1-48742946-G-C
• rs1934393
• NM_032785.4:c.635-79705C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_032785.4(AGBL4):​c.635-79705C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,088 control chromosomes in the GnomAD database, including 29,932 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 0.59 (29932 hom., cov: 33)
• Consequence: AGBL4 NM_032785.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43
• Publications: 9 publications found

Genes affected

AGBL4 (HGNC:25892): (AGBL carboxypeptidase 4) Predicted to enable metallocarboxypeptidase activity and tubulin binding activity. Predicted to be involved in C-terminal protein deglutamylation; defense response to virus; and protein side chain deglutamylation. Predicted to act upstream of or within several processes, including axonal transport of mitochondrion; positive regulation of ubiquitin-dependent protein catabolic process; and regulation of blastocyst development. Located in Golgi apparatus; centriole; and ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

BEND5 (HGNC:25668): (BEN domain containing 5) Predicted to enable DNA binding activity. Involved in negative regulation of transcription, DNA-templated. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032785.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGBL4	NM_032785.4	MANE Select	c.635-79705C>G		intron	N/A	NP_116174.3
	BEND5	NM_024603.4	MANE Select	c.746-175C>G		intron	N/A	NP_078879.2
	AGBL4	NM_001323574.2		c.671-79705C>G		intron	N/A	NP_001310503.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGBL4	ENST00000371839.6	TSL:2 MANE Select	c.635-79705C>G		intron	N/A	ENSP00000360905.1
	BEND5	ENST00000371833.4	TSL:1 MANE Select	c.746-175C>G		intron	N/A	ENSP00000360899.3
	AGBL4	ENST00000416121.5	TSL:1	c.170-79705C>G		intron	N/A	ENSP00000401622.1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90207 AN: 151970 Hom.: 29921 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.593 AC: 90230 AN: 152088 Hom.: 29932 Cov.: 33 AF XY: 0.584 AC XY: 43397 AN XY: 74350

African (AFR) AF: 0.314 AC: 13005 AN: 41460

American (AMR) AF: 0.585 AC: 8941 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2689 AN: 3466

East Asian (EAS) AF: 0.270 AC: 1397 AN: 5168

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4818

European-Finnish (FIN) AF: 0.656 AC: 6935 AN: 10572

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52504 AN: 68004

Other (OTH) AF: 0.628 AC: 1322 AN: 2106

Alfa AF: 0.578 Hom.: 1990

Bravo AF: 0.575

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	17
DANN	Benign	0.61
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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: rs1934393; hg19: chr1-49208618;