17-3802232-C-T

Position:

• chr17-3802232-C-T

Variant summary

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

The NM_001114118.3(NCBP3):​c.*10812G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,002 control chromosomes in the GnomAD database, including 30,628 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 0.61 (30628 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: NCBP3 NM_001114118.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

NCBP3 (HGNC:24612): (nuclear cap binding subunit 3) Enables RNA 7-methylguanosine cap binding activity and mRNA binding activity. Involved in defense response to virus. Located in cytoplasm and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NCBP3	NM_001114118.3	c.*10812G>A		3_prime_UTR_variant	13/13	ENST00000389005.6
NCBP3	NM_001398494.1	c.*10314G>A		3_prime_UTR_variant	14/14
NCBP3	XR_007065313.1	n.2224G>A		non_coding_transcript_exon_variant	15/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NCBP3	ENST00000389005.6	c.*10812G>A		3_prime_UTR_variant	13/13	5	NM_001114118.3	P1
NCBP3	ENST00000572988.1	n.451G>A		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92745 AN: 151880 Hom.: 30561 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.540

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.611 AC: 92870 AN: 151998 Hom.: 30628 Cov.: 32 AF XY: 0.607 AC XY: 45093 AN XY: 74270

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.541

Alfa AF: 0.509 Hom.: 26747

Bravo AF: 0.622

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.62

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: rs2891; hg19: chr17-3705526;