2-135197227-T-C

Variant names:

• chr2-135197227-T-C
• rs1375131
• NM_032143.4:c.*3115A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032143.4(ZRANB3):​c.*3115A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,160 control chromosomes in the GnomAD database, including 33,633 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 0.61 (33633 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ZRANB3 NM_032143.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032143.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZRANB3	NM_032143.4	MANE Select	c.*3115A>G		3_prime_UTR	Exon 21 of 21	NP_115519.2
	ZRANB3	NM_001286568.2		c.*3115A>G		3_prime_UTR	Exon 21 of 21	NP_001273497.1
	ZRANB3	NM_001286569.1		c.*3115A>G		3_prime_UTR	Exon 22 of 22	NP_001273498.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZRANB3	ENST00000264159.11	TSL:1 MANE Select	c.*3115A>G		3_prime_UTR	Exon 21 of 21	ENSP00000264159.6
	ZRANB3	ENST00000401392.5	TSL:1	c.*3115A>G		3_prime_UTR	Exon 21 of 21	ENSP00000383979.1
	ZRANB3	ENST00000536680.5	TSL:1	c.*3115A>G		3_prime_UTR	Exon 22 of 22	ENSP00000441320.2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92775 AN: 152042 Hom.: 33567 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.706

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.611 AC: 92905 AN: 152160 Hom.: 33633 Cov.: 32 AF XY: 0.625 AC XY: 46520 AN XY: 74402

African (AFR) AF: 0.881 AC: 36600 AN: 41528

American (AMR) AF: 0.779 AC: 11905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3025 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5182

South Asian (SAS) AF: 0.823 AC: 3968 AN: 4822

European-Finnish (FIN) AF: 0.426 AC: 4513 AN: 10584

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25698 AN: 67986

Other (OTH) AF: 0.710 AC: 1493 AN: 2104

Alfa AF: 0.465 Hom.: 14693

Bravo AF: 0.649

Asia WGS AF: 0.923 AC: 3209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.78
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1375131; hg19: chr2-135954797;