5-176348308-C-T

Variant names:

• chr5-176348308-C-T
• NM_020444.5:c.508G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020444.5(KIAA1191):​c.508G>A​(p.Ala170Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 30)
• Consequence: KIAA1191 NM_020444.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.03
• Publications: 0 publications found

Genes affected

KIAA1191 (HGNC:29209): (KIAA1191) Predicted to enable oxidoreductase activity. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

KIAA1191-AS1 (HGNC:41234):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1818741).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020444.5. 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
	KIAA1191	NM_020444.5	MANE Select	c.508G>A	p.Ala170Thr	missense	Exon 7 of 9	NP_065177.2
	KIAA1191	NM_001079685.3		c.508G>A	p.Ala170Thr	missense	Exon 6 of 8	NP_001073153.1	Q96A73-1
	KIAA1191	NM_001079684.3		c.451G>A	p.Ala151Thr	missense	Exon 6 of 8	NP_001073152.1	Q96A73-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1191	ENST00000298569.9	TSL:1 MANE Select	c.508G>A	p.Ala170Thr	missense	Exon 7 of 9	ENSP00000298569.4	Q96A73-1
	KIAA1191	ENST00000510164.5	TSL:1	c.508G>A	p.Ala170Thr	missense	Exon 6 of 8	ENSP00000421061.1	Q96A73-1
	KIAA1191	ENST00000393725.6	TSL:1	c.451G>A	p.Ala151Thr	missense	Exon 6 of 8	ENSP00000377326.2	Q96A73-2

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 30

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	0.077
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	18
DANN	Benign	0.77
DEOGEN2	Benign	0.012	T
Eigen	Uncertain	0.33
Eigen_PC	Uncertain	0.39
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.85	T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.18	T
MetaSVM	Benign	-0.97	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		4.0
PrimateAI	Benign	0.33	T
PROVEAN	Benign	-0.76	N
REVEL	Benign	0.10
Sift	Benign	0.30	T
Sift4G	Benign	0.55	T
Polyphen		0.78	P
Vest4		0.11
MutPred		0.092		Gain of glycosylation at A170 (P = 0.0032)
MVP		0.55
MPC		0.64
ClinPred		0.60	D
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2
Varity_R		0.073
gMVP		0.11
Mutation Taster		=81/19	polymorphism

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: chr5-175775311;