ENST00000443534.1:n.881A>C

Variant names:

• chr10-45236012-T-G
• rs4948970
• ENST00000443534.1:n.881A>C

Variant summary

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

The ENST00000443534.1(CUBNP2):​n.881A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 1,373,082 control chromosomes in the GnomAD database, including 365,400 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 0.71 (39315 hom., cov: 30)
  • Exomes 𝑓: 0.72 (326085 hom.)
• Consequence: CUBNP2 ENST00000443534.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884
• Publications: 2 publications found

Genes affected

CUBNP2 (HGNC:44984): (cubilin pseudogene 2)

ZNF22-AS1 (HGNC:23509): (ZNF22 antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000243349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000443534.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUBNP2	ENST00000443534.1	TSL:6	n.881A>C		non_coding_transcript_exon	Exon 6 of 7
	ZNF22-AS1	ENST00000745492.1		n.82A>C		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000243349	ENST00000745710.1		n.621-3665T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.707 AC: 105784 AN: 149578 Hom.: 39287 Cov.: 30

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.698

GnomAD4 exome AF: 0.720 AC: 881034 AN: 1223388 Hom.: 326085 Cov.: 22 AF XY: 0.712 AC XY: 441164 AN XY: 619770

African (AFR) AF: 0.691 AC: 18450 AN: 26698

American (AMR) AF: 0.766 AC: 33915 AN: 44284

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 16646 AN: 24744

East Asian (EAS) AF: 0.279 AC: 10794 AN: 38648

South Asian (SAS) AF: 0.487 AC: 39672 AN: 81382

European-Finnish (FIN) AF: 0.751 AC: 39962 AN: 53242

Middle Eastern (MID) AF: 0.670 AC: 3499 AN: 5226

European-Non Finnish (NFE) AF: 0.760 AC: 681575 AN: 896874

Other (OTH) AF: 0.698 AC: 36521 AN: 52290

GnomAD4 genome AF: 0.707 AC: 105856 AN: 149694 Hom.: 39315 Cov.: 30 AF XY: 0.701 AC XY: 51336 AN XY: 73200

African (AFR) AF: 0.692 AC: 27157 AN: 39222

American (AMR) AF: 0.763 AC: 11605 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2323 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1183 AN: 5162

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4820

European-Finnish (FIN) AF: 0.751 AC: 7928 AN: 10562

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51076 AN: 67970

Other (OTH) AF: 0.690 AC: 1439 AN: 2086

Alfa AF: 0.634 Hom.: 1756

Bravo AF: 0.712

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.27
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs4948970; hg19: chr10-45731460;