rs868274019

Variant names:

• chr17-4988511-C-A
• rs868274019
• NM_001394789.1:c.605G>T

Your query was ambiguous. Multiple possible variants found:

• chr17-4988511-C-A
• chr17-4988511-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001394789.1(INCA1):​c.605G>T​(p.Cys202Phe) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C202Y) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: INCA1 NM_001394789.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

INCA1 (HGNC:32224): (inhibitor of CDK, cyclin A1 interacting protein 1) Enables cyclin binding activity; cyclin-dependent protein serine/threonine kinase inhibitor activity; and identical protein binding activity. Acts upstream of or within negative regulation of cyclin-dependent protein serine/threonine kinase activity. Located in cytoplasm and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000262227 (HGNC:):

CAMTA2-AS1 (HGNC:55342): (CAMTA2 antisense RNA 1)

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=0.100138664).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
INCA1	NM_001394789.1	c.605G>T	p.Cys202Phe	missense_variant	Exon 7 of 7	ENST00000695324.1	NP_001381718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
INCA1	ENST00000695324.1	c.605G>T	p.Cys202Phe	missense_variant	Exon 7 of 7		NM_001394789.1	ENSP00000511805.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.040	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	14
DANN	Benign	0.95
DEOGEN2	Uncertain	0.49	.;.;T;T
Eigen	Benign	-0.82
Eigen_PC	Benign	-0.88
FATHMM_MKL	Benign	0.031	N
LIST_S2	Benign	0.39	.;T;.;T
M_CAP	Benign	0.0037	T
MetaRNN	Benign	0.10	T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.8	.;.;L;L
PrimateAI	Benign	0.31	T
PROVEAN	Pathogenic	-7.0	D;.;.;.
REVEL	Benign	0.13
Sift	Benign	0.090	T;.;.;.
Sift4G	Benign	0.11	T;T;T;T
Polyphen		0.24	B;B;B;B
Vest4		0.17
MutPred		0.27		.;.;Gain of helix (P = 0.0425);Gain of helix (P = 0.0425);
MVP		0.12
ClinPred		0.13	T
GERP RS		1.3
Varity_R		0.13
gMVP		0.050

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs868274019; hg19: chr17-4891806;