rs73592376

chr10-16895788-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001081.4(CUBN):c.8598+3208C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,016 control chromosomes in the GnomAD database, including 3,773 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 0.18 (3773 hom., cov: 32)
• Consequence: CUBN NM_001081.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

CUBN (HGNC:2548): (cubilin) Cubilin (CUBN) acts as a receptor for intrinsic factor-vitamin B12 complexes. The role of receptor is supported by the presence of 27 CUB domains. Cubulin is located within the epithelium of intestine and kidney. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CUBN	NM_001081.4	c.8598+3208C>A		intron_variant		ENST00000377833.10
CUBN	XM_011519709.3	c.4584+3208C>A		intron_variant
CUBN	XM_011519710.3	c.4560+3208C>A		intron_variant
CUBN	XM_011519711.4	c.4440+3208C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CUBN	ENST00000377833.10	c.8598+3208C>A		intron_variant		1	NM_001081.4	P1

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27544 AN: 151896 Hom.: 3747 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.182 AC: 27609 AN: 152016 Hom.: 3773 Cov.: 32 AF XY: 0.176 AC XY: 13098 AN XY: 74298

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.170

Alfa AF: 0.153 Hom.: 335

Bravo AF: 0.194

Asia WGS AF: 0.0810 AC: 284 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.0
Dann	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs73592376; hg19: chr10-16937787;