6-33417536-C-T

Position:

• chr6-33417536-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 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. 14/20 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

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

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.14274517).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CUTA	NM_001014840.2	c.202G>A	p.Val68Ile	missense_variant	2/6	ENST00000488034.6	NP_001014840.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUTA	ENST00000488034.6	c.202G>A	p.Val68Ile	missense_variant	2/6	2	NM_001014840.2	ENSP00000417544	A1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

New York Genome Center

Jun 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

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;.;T;.;.;.
Eigen	Benign	-0.19
Eigen_PC	Benign	-0.065
FATHMM_MKL	Benign	0.70	D
LIST_S2	Benign	0.82	T;T;T;.;T;D;.;.
M_CAP	Benign	0.0057	T
MetaRNN	Benign	0.14	T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	1.1	.;.;L;.;.;.;.;.
MutationTaster	Benign	0.98	N;N;N;N;N;N
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.030	N;.;N;.;N;N;N;N
REVEL	Benign	0.053
Sift	Benign	0.064	T;.;T;.;T;T;T;T
Sift4G	Benign	0.15	T;T;T;T;T;T;T;T
Polyphen		0.082	B;.;B;.;.;.;.;.
Vest4		0.19
MutPred		0.45		.;.;Loss of disorder (P = 0.1096);.;.;Loss of disorder (P = 0.1096);.;.;
MVP		0.22
MPC		0.31
ClinPred		0.69	D
GERP RS		5.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.16
gMVP		0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-33385313;