chr6-33417536-C-T

Variant names:

• chr6-33417536-C-T
• NM_001014840.2:c.202G>A

Variant summary

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

The NM_001014840.2(CUTA):​c.202G>A​(p.Val68Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CUTA NM_001014840.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.19
• Publications: 0 publications found

Genes affected

CUTA (HGNC:21101): (cutA divalent cation tolerance homolog) Enables enzyme binding activity. Involved in protein localization. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=0.14274517).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001014840.2. 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
	CUTA	NM_001014840.2	MANE Select	c.202G>A	p.Val68Ile	missense	Exon 2 of 6	NP_001014840.1	O60888-1
	CUTA	NM_001014433.3		c.133G>A	p.Val45Ile	missense	Exon 2 of 6	NP_001014433.2	O60888-3
	CUTA	NM_001014837.2		c.133G>A	p.Val45Ile	missense	Exon 2 of 6	NP_001014837.1	O60888-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUTA	ENST00000488034.6	TSL:2 MANE Select	c.202G>A	p.Val68Ile	missense	Exon 2 of 6	ENSP00000417544.1	O60888-1
	CUTA	ENST00000374500.10	TSL:1	c.133G>A	p.Val45Ile	missense	Exon 2 of 6	ENSP00000363624.6	O60888-3
	CUTA	ENST00000440279.7	TSL:1	c.133G>A	p.Val45Ile	missense	Exon 1 of 5	ENSP00000403268.2	O60888-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.096	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Uncertain	0.98
DEOGEN2	Benign	0.031	T
Eigen	Benign	-0.19
Eigen_PC	Benign	-0.065
FATHMM_MKL	Benign	0.70	D
LIST_S2	Benign	0.82	T
M_CAP	Benign	0.0057	T
MetaRNN	Benign	0.14	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.1	L
PhyloP100		2.2
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.030	N
REVEL	Benign	0.053
Sift	Benign	0.064	T
Sift4G	Benign	0.15	T
Polyphen		0.082	B
Vest4		0.19
MutPred		0.45		Loss of disorder (P = 0.1096)
MVP		0.22
MPC		0.31
ClinPred		0.69	D
GERP RS		5.1
PromoterAI		0.036	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.16
gMVP		0.18
Mutation Taster		=85/15	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: chr6-33385313;