rs2796188

Variant names:

• chr1-71229178-G-A
• rs2796188
• ENST00000455406.6:n.189+6064G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-71229178-G-A
• chr1-71229178-G-T

Variant summary

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

The ENST00000455406.6(ZRANB2-DT):​n.189+6064G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,934 control chromosomes in the GnomAD database, including 18,423 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 0.49 (18423 hom., cov: 32)
• Consequence: ZRANB2-DT ENST00000455406.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 5 publications found

Genes affected

ZRANB2-DT (HGNC:43595): (ZRANB2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZRANB2-DT	NR_046217.1	n.189+6064G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZRANB2-DT	ENST00000455406.6	n.189+6064G>A		intron_variant	Intron 3 of 3	1
ZRANB2-DT	ENST00000413421.5	n.434+6064G>A		intron_variant	Intron 6 of 7	3
ZRANB2-DT	ENST00000415780.1	n.180+6064G>A		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74305 AN: 151818 Hom.: 18412 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.489 AC: 74333 AN: 151934 Hom.: 18423 Cov.: 32 AF XY: 0.487 AC XY: 36132 AN XY: 74234

African (AFR) AF: 0.482 AC: 19966 AN: 41426

American (AMR) AF: 0.476 AC: 7275 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1872 AN: 3466

East Asian (EAS) AF: 0.258 AC: 1325 AN: 5144

South Asian (SAS) AF: 0.439 AC: 2116 AN: 4816

European-Finnish (FIN) AF: 0.464 AC: 4895 AN: 10540

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35106 AN: 67960

Other (OTH) AF: 0.493 AC: 1038 AN: 2106

Alfa AF: 0.506 Hom.: 84515

Bravo AF: 0.485

Asia WGS AF: 0.403 AC: 1403 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.74
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs2796188; hg19: chr1-71694861;