rs755632125

Variant names:

• chr16-22534471-C-T
• rs755632125
• NM_001395849.1:c.1488C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BP7

The NM_001395849.1(NPIPB5):​c.1488C>T​(p.Ala496Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.00027 (0 hom., cov: 20)
  • Exomes 𝑓: 0.000034 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NPIPB5 NM_001395849.1 synonymous
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.105

Genes affected

NPIPB5 (HGNC:37233): (nuclear pore complex interacting protein family member B5) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC105371131 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 16-22534471-C-T is Benign according to our data. Variant chr16-22534471-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 403260.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.105 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NPIPB5	NM_001395849.1	c.1488C>T	p.Ala496Ala	synonymous_variant	Exon 7 of 7	ENST00000424340.7	NP_001382778.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NPIPB5	ENST00000424340.7	c.1488C>T	p.Ala496Ala	synonymous_variant	Exon 7 of 7	1	NM_001395849.1	ENSP00000440703.1

Frequencies

GnomAD3 genomes AF: 0.000272 AC: 32 AN: 117504 Hom.: 0 Cov.: 20

Gnomad AFR AF: 0.000233

Gnomad AMI AF: 0.00154

Gnomad AMR AF: 0.0000852

Gnomad ASJ AF: 0.000342

Gnomad EAS AF: 0.000311

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.000133

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000266

Gnomad OTH AF: 0.000635

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000339 AC: 28 AN: 826670 Hom.: 0 Cov.: 19 AF XY: 0.0000439 AC XY: 19 AN XY: 432852

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000251

Gnomad4 ASJ exome AF: 0.0000480

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000211

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000146

Gnomad4 OTH exome AF: 0.0000776

GnomAD4 genome AF: 0.000272 AC: 32 AN: 117592 Hom.: 0 Cov.: 20 AF XY: 0.000297 AC XY: 17 AN XY: 57204

Gnomad4 AFR AF: 0.000232

Gnomad4 AMR AF: 0.0000851

Gnomad4 ASJ AF: 0.000342

Gnomad4 EAS AF: 0.000311

Gnomad4 SAS AF: 0.00123

Gnomad4 FIN AF: 0.000133

Gnomad4 NFE AF: 0.000266

Gnomad4 OTH AF: 0.000634

Alfa AF: 0.0000843 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent variant not near splice site -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.71

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: rs755632125; hg19: chr16-22545792; COSMIC: COSV69995071; COSMIC: COSV69995071;