19-17527341-A-T

Variant names:

• chr19-17527341-A-T
• ENST00000335393.8:c.94A>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001321828.1(NIBAN3):​c.-598A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: NIBAN3 NM_001321828.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.07
• Publications: 0 publications found

Genes affected

NIBAN3 (HGNC:24130): (niban apoptosis regulator 3)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321828.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIBAN3	NM_001321827.2	MANE Select	c.1A>T	p.Met1?	initiator_codon	Exon 1 of 15	NP_001308756.2	M0QXK3
	NIBAN3	NM_001321828.1		c.-598A>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 14	NP_001308757.1	Q86XR2-6
	NIBAN3	NM_173544.5		c.94A>T	p.Met32Leu	missense	Exon 2 of 16	NP_775815.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIBAN3	ENST00000335393.8	TSL:1	c.94A>T	p.Met32Leu	missense	Exon 2 of 16	ENSP00000335040.3	Q86XR2-1
	NIBAN3	ENST00000595684.5	TSL:1	c.94A>T	p.Met32Leu	missense	Exon 2 of 15	ENSP00000470106.1	Q86XR2-2
	NIBAN3	ENST00000332386.9	TSL:1	c.94A>T	p.Met32Leu	missense	Exon 2 of 16	ENSP00000333447.4	Q86XR2-3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 31

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.050	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	23
DANN	Benign	0.92
DEOGEN2	Benign	0.022	T
Eigen	Benign	0.13
Eigen_PC	Benign	0.0075
FATHMM_MKL	Benign	0.30	N
LIST_S2	Benign	0.49	T
M_CAP	Benign	0.048	D
MetaRNN	Uncertain	0.46	T
MetaSVM	Benign	-0.90	T
MutationAssessor	Benign	0.90	L
PhyloP100		3.1
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-1.8	N
REVEL	Benign	0.21
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		0.80	P
Vest4		0.63
MutPred		0.41		Gain of glycosylation at S31 (P = 0.0474)
MVP		0.23
MPC		0.40
ClinPred		0.69	D
GERP RS		3.1
PromoterAI		0.0015	Neutral
Varity_R		0.93
gMVP		0.47
Mutation Taster		=69/131	disease causing

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

hg19: chr19-17638150;