17-3802232-C-T

Variant names:

• chr17-3802232-C-T
• rs2891
• NM_001114118.3:c.*10812G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114118.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCBP3	NM_001114118.3	MANE Select	c.*10812G>A		3_prime_UTR	Exon 13 of 13	NP_001107590.1
	NCBP3	NM_001398494.1		c.*10314G>A		3_prime_UTR	Exon 14 of 14	NP_001385423.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NCBP3	ENST00000389005.6	TSL:5 MANE Select	c.*10812G>A		3_prime_UTR	Exon 13 of 13	ENSP00000373657.4
	NCBP3	ENST00000572988.1	TSL:3	n.451G>A		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.885 AC: 36743 AN: 41500

American (AMR) AF: 0.564 AC: 8604 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1652 AN: 5170

South Asian (SAS) AF: 0.501 AC: 2411 AN: 4812

European-Finnish (FIN) AF: 0.567 AC: 5969 AN: 10526

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34133 AN: 67950

Other (OTH) AF: 0.541 AC: 1136 AN: 2100

Alfa AF: 0.538 Hom.: 51847

Bravo AF: 0.622

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.62
PhyloP100		-0.17

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

Other links and lift over

dbSNP: rs2891; hg19: chr17-3705526;