chr9-104769675-C-T

Position:

• chr9-104769675-C-T

Variant summary

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

The NM_018376.4(NIPSNAP3B):​c.430+654C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,968 control chromosomes in the GnomAD database, including 32,528 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 0.65 (32528 hom., cov: 32)
• Consequence: NIPSNAP3B NM_018376.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120

Genes affected

NIPSNAP3B (HGNC:23641): (nipsnap homolog 3B) NIPSNAP3B belongs to a family of proteins with putative roles in vesicular trafficking (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008]

NIPSNAP3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIPSNAP3B	NM_018376.4	c.430+654C>T		intron_variant		ENST00000374762.4	NP_060846.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIPSNAP3B	ENST00000374762.4	c.430+654C>T		intron_variant		1	NM_018376.4	ENSP00000363894.3
NIPSNAP3B	ENST00000460936.5	n.430+654C>T		intron_variant		5		ENSP00000435209.1
NIPSNAP3B	ENST00000461177.1	n.265+654C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98623 AN: 151850 Hom.: 32498 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.679

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.650 AC: 98704 AN: 151968 Hom.: 32528 Cov.: 32 AF XY: 0.644 AC XY: 47858 AN XY: 74266

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.672

Alfa AF: 0.635 Hom.: 58956

Bravo AF: 0.672

Asia WGS AF: 0.533 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.78

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: rs2472476; hg19: chr9-107531956;