9-104765635-G-A

Position:

• chr9-104765635-G-A

Variant summary

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

The NM_018376.4(NIPSNAP3B):​c.61-690G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,056 control chromosomes in the GnomAD database, including 14,492 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 0.41 (14492 hom., cov: 32)
• Consequence: NIPSNAP3B NM_018376.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIPSNAP3B	NM_018376.4	c.61-690G>A		intron_variant		ENST00000374762.4	NP_060846.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIPSNAP3B	ENST00000374762.4	c.61-690G>A		intron_variant		1	NM_018376.4	ENSP00000363894	P1
NIPSNAP3B	ENST00000460936.5	c.61-690G>A		intron_variant, NMD_transcript_variant		5		ENSP00000435209
NIPSNAP3B	ENST00000461177.1	n.106+1335G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62225 AN: 151938 Hom.: 14485 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.409 AC: 62254 AN: 152056 Hom.: 14492 Cov.: 32 AF XY: 0.404 AC XY: 30015 AN XY: 74300

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.458

Alfa AF: 0.510 Hom.: 19028

Bravo AF: 0.402

Asia WGS AF: 0.188 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.74

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: rs2487714; hg19: chr9-107527916;