rs1059177

Positions:

• chr16-14765236-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001395485.2(NPIPA2):​c.933T>C​(p.Cys311=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0020 (0 hom., cov: 18)
  • Exomes 𝑓: 0.00029 (8 hom.)
  • Failed GnomAD Quality Control
• Consequence: NPIPA2 NM_001395485.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

Genes affected

NPIPA2 (HGNC:41979): (nuclear pore complex interacting protein family member A2) Predicted to be involved in mRNA transport and protein transport. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BP7: Synonymous conserved (PhyloP=-2.22 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NPIPA2	NM_001395485.2	c.933T>C	p.Cys311=	synonymous_variant	10/10	ENST00000529166.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NPIPA2	ENST00000529166.6	c.933T>C	p.Cys311=	synonymous_variant	10/10	5	NM_001395485.2	P1
NPIPA2	ENST00000553201.1	c.876T>C	p.Cys292=	synonymous_variant	8/8	1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 249 AN: 123100 Hom.: 0 Cov.: 18 FAILED QC

Gnomad AFR AF: 0.00643

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00107

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000185

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000827 AC: 50 AN: 60458 Hom.: 1 AF XY: 0.000609 AC XY: 18 AN XY: 29578

Gnomad AFR exome AF: 0.00783

Gnomad AMR exome AF: 0.000365

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000504

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000288 AC: 398 AN: 1381774 Hom.: 8 Cov.: 28 AF XY: 0.000243 AC XY: 168 AN XY: 690808

Gnomad4 AFR exome AF: 0.00856

Gnomad4 AMR exome AF: 0.000877

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000704

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000123

Gnomad4 OTH exome AF: 0.00103

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00204 AC: 251 AN: 123188 Hom.: 0 Cov.: 18 AF XY: 0.00202 AC XY: 120 AN XY: 59394

Gnomad4 AFR AF: 0.00647

Gnomad4 AMR AF: 0.00107

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000185

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00341 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.32

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: rs1059177; hg19: chr16-14859093;