rs1561277

Variant names:

• chr2-135334491-C-A
• rs1561277
• NM_032143.4:c.677+11059G>T

Your query was ambiguous. Multiple possible variants found:

• chr2-135334491-C-A
• chr2-135334491-C-G
• chr2-135334491-C-T

Variant summary

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

The NM_032143.4(ZRANB3):​c.677+11059G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,062 control chromosomes in the GnomAD database, including 30,916 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 0.58 (30916 hom., cov: 32)
• Consequence: ZRANB3 NM_032143.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 18 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZRANB3	NM_032143.4	c.677+11059G>T		intron_variant	Intron 6 of 20	ENST00000264159.11	NP_115519.2
ZRANB3	NM_001286568.2	c.677+11059G>T		intron_variant	Intron 6 of 20		NP_001273497.1
ZRANB3	NM_001286569.1	c.-781+11059G>T		intron_variant	Intron 6 of 21		NP_001273498.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZRANB3	ENST00000264159.11	c.677+11059G>T		intron_variant	Intron 6 of 20	1	NM_032143.4	ENSP00000264159.6

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87753 AN: 151944 Hom.: 30854 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.578 AC: 87879 AN: 152062 Hom.: 30916 Cov.: 32 AF XY: 0.590 AC XY: 43857 AN XY: 74310

African (AFR) AF: 0.875 AC: 36312 AN: 41500

American (AMR) AF: 0.718 AC: 10953 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2834 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5173 AN: 5190

South Asian (SAS) AF: 0.746 AC: 3591 AN: 4812

European-Finnish (FIN) AF: 0.355 AC: 3731 AN: 10522

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23366 AN: 67988

Other (OTH) AF: 0.660 AC: 1395 AN: 2114

Alfa AF: 0.408 Hom.: 12244

Bravo AF: 0.616

Asia WGS AF: 0.893 AC: 3104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.67
PhyloP100		1.0
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: rs1561277; hg19: chr2-136092061;