rs7202

chr14-73275573-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001005743.2(NUMB):c.*1005C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,892 control chromosomes in the GnomAD database, including 4,911 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 0.25 (4911 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NUMB NM_001005743.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.949

Genes affected

NUMB (HGNC:8060): (NUMB endocytic adaptor protein) The protein encoded by this gene plays a role in the determination of cell fates during development. The encoded protein, whose degradation is induced in a proteasome-dependent manner by MDM2, is a membrane-bound protein that has been shown to associate with EPS15, LNX1, and NOTCH1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NUMB	NM_001005743.2	c.*1005C>T		3_prime_UTR_variant	13/13	ENST00000555238.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NUMB	ENST00000555238.6	c.*1005C>T		3_prime_UTR_variant	13/13	1	NM_001005743.2	P4

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38284 AN: 151774 Hom.: 4912 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.249

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.252 AC: 38305 AN: 151892 Hom.: 4911 Cov.: 32 AF XY: 0.250 AC XY: 18572 AN XY: 74224

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.251

Alfa AF: 0.279 Hom.: 3138

Bravo AF: 0.251

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
Cadd	Benign	11
Dann	Benign	0.87

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: rs7202; hg19: chr14-73742281;