rs10128001

Positions:

• chr1-71079156-C-T

Variant summary

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

The NM_203350.3(ZRANB2):​c.57-448G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,242 control chromosomes in the GnomAD database, including 1,925 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 0.13 (1925 hom., cov: 32)
• Consequence: ZRANB2 NM_203350.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

Genes affected

ZRANB2 (HGNC:13058): (zinc finger RANBP2-type containing 2) Enables RNA binding activity. Predicted to be involved in RNA splicing and mRNA processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZRANB2	NM_203350.3	c.57-448G>A		intron_variant		ENST00000370920.8	NP_976225.1
ZRANB2	NM_005455.5	c.57-448G>A		intron_variant			NP_005446.2
ZRANB2	XM_047434733.1	c.57-448G>A		intron_variant			XP_047290689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZRANB2	ENST00000370920.8	c.57-448G>A		intron_variant		1	NM_203350.3	ENSP00000359958	A1
ZRANB2	ENST00000254821.10	c.57-448G>A		intron_variant		1		ENSP00000254821	P4
ZRANB2	ENST00000611683.1	c.57-448G>A		intron_variant		2		ENSP00000482026	P4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19382 AN: 151124 Hom.: 1920 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.128 AC: 19421 AN: 151242 Hom.: 1925 Cov.: 32 AF XY: 0.122 AC XY: 9021 AN XY: 73962

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.0441

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0973 Hom.: 887

Bravo AF: 0.138

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.23

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: rs10128001; hg19: chr1-71544839;