rs10901841

Positions:

• chr10-124943817-C-A
• chr10-124943817-C-G
• chr10-124943817-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017580.3(ZRANB1):​c.814+510C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,018 control chromosomes in the GnomAD database, including 30,461 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 (30461 hom., cov: 32)
• Consequence: ZRANB1 NM_017580.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636

Genes affected

ZRANB1 (HGNC:18224): (zinc finger RANBP2-type containing 1) Enables K63-linked polyubiquitin modification-dependent protein binding activity and thiol-dependent deubiquitinase. Involved in several processes, including positive regulation of Wnt signaling pathway; protein deubiquitination; and regulation of cell morphogenesis. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -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 = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZRANB1	NM_017580.3	c.814+510C>A		intron_variant		ENST00000359653.4	NP_060050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZRANB1	ENST00000359653.4	c.814+510C>A		intron_variant		1	NM_017580.3	ENSP00000352676	P1

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90223 AN: 151900 Hom.: 30472 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.594 AC: 90223 AN: 152018 Hom.: 30461 Cov.: 32 AF XY: 0.594 AC XY: 44132 AN XY: 74278

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.625

Alfa AF: 0.701 Hom.: 9046

Bravo AF: 0.563

Asia WGS AF: 0.682 AC: 2372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	18
DANN	Benign	0.80

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: rs10901841; hg19: chr10-126632386;