rs935612

Variant names:

• chr2-135183933-A-G
• rs935612
• ENST00000412849.5:n.1781+16421T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-135183933-A-G
• chr2-135183933-A-T

Variant summary

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

The ENST00000619650.4(ZRANB3):​c.1617+16421T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,138 control chromosomes in the GnomAD database, including 9,152 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 0.27 (9152 hom., cov: 32)
• Consequence: ZRANB3 ENST00000619650.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.682

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZRANB3	ENST00000412849.5	n.1781+16421T>C		intron_variant	Intron 10 of 13	1
ZRANB3	ENST00000619650.4	c.1617+16421T>C		intron_variant	Intron 9 of 12	5		ENSP00000480120.1

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40828 AN: 152020 Hom.: 9123 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.0793

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.269 AC: 40908 AN: 152138 Hom.: 9152 Cov.: 32 AF XY: 0.269 AC XY: 20003 AN XY: 74422

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.0738

Gnomad4 NFE AF: 0.0993

Gnomad4 OTH AF: 0.258

Alfa AF: 0.169 Hom.: 1210

Bravo AF: 0.295

Asia WGS AF: 0.315 AC: 1094 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	0.53
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs935612; hg19: chr2-135941503;