10-45236012-T-G

Position:

• chr10-45236012-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUBNP2	ENST00000443534.1	n.881A>C		non_coding_transcript_exon_variant	6/7

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

Gnomad4 AFR exome AF: 0.691

Gnomad4 AMR exome AF: 0.766

Gnomad4 ASJ exome AF: 0.673

Gnomad4 EAS exome AF: 0.279

Gnomad4 SAS exome AF: 0.487

Gnomad4 FIN exome AF: 0.751

Gnomad4 NFE exome AF: 0.760

Gnomad4 OTH exome AF: 0.698

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

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.690

Alfa AF: 0.634 Hom.: 1715

Bravo AF: 0.712

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4948970; hg19: chr10-45731460;