rs10128001

Variant names:

• chr1-71079156-C-T
• rs10128001
• NM_203350.3:c.57-448G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ZRANB2	NM_203350.3	c.57-448G>A		intron_variant	Intron 1 of 9	ENST00000370920.8	NP_976225.1
ZRANB2	NM_005455.5	c.57-448G>A		intron_variant	Intron 1 of 10		NP_005446.2
ZRANB2	XM_047434733.1	c.57-448G>A		intron_variant	Intron 1 of 9		XP_047290689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZRANB2	ENST00000370920.8	c.57-448G>A		intron_variant	Intron 1 of 9	1	NM_203350.3	ENSP00000359958.3
ZRANB2	ENST00000254821.10	c.57-448G>A		intron_variant	Intron 1 of 10	1		ENSP00000254821.6
ZRANB2	ENST00000611683.1	c.57-448G>A		intron_variant	Intron 1 of 9	2		ENSP00000482026.1

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

African (AFR) AF: 0.276 AC: 11222 AN: 40658

American (AMR) AF: 0.0802 AC: 1223 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3466

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4824

European-Finnish (FIN) AF: 0.0441 AC: 467 AN: 10588

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0834 AC: 5670 AN: 67950

Other (OTH) AF: 0.136 AC: 286 AN: 2106

Alfa AF: 0.104 Hom.: 1412

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
PhyloP100		-1.1
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: rs10128001; hg19: chr1-71544839;