rs2118395

Positions:

• chr2-135443750-A-T

Variant summary

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

The NM_032143.4(ZRANB3):​c.162-52930T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,144 control chromosomes in the GnomAD database, including 1,088 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 0.10 (1088 hom., cov: 32)
• Consequence: ZRANB3 NM_032143.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

Genes affected

ZRANB3 (HGNC:25249): (zinc finger RANBP2-type containing 3) Enables ATP-dependent DNA/DNA annealing activity; K63-linked polyubiquitin modification-dependent protein binding activity; and endodeoxyribonuclease activity. Involved in several processes, including DNA metabolic process; DNA rewinding; and negative regulation of DNA recombination. Located in nuclear replication fork and 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=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZRANB3	NM_032143.4	c.162-52930T>A		intron_variant		ENST00000264159.11	NP_115519.2
ZRANB3	NM_001286568.2	c.162-52930T>A		intron_variant			NP_001273497.1
ZRANB3	NM_001286569.1	c.-1296-52930T>A		intron_variant			NP_001273498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZRANB3	ENST00000264159.11	c.162-52930T>A		intron_variant		1	NM_032143.4	ENSP00000264159	P4

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15827 AN: 152026 Hom.: 1092 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.104 AC: 15833 AN: 152144 Hom.: 1088 Cov.: 32 AF XY: 0.109 AC XY: 8133 AN XY: 74374

Gnomad4 AFR AF: 0.0909

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.0767

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0876 Hom.: 86

Bravo AF: 0.109

Asia WGS AF: 0.248 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.0
DANN	Benign	0.89

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: rs2118395; hg19: chr2-136201320;