2-196676618-G-T

Variant names:

• chr2-196676618-G-T
• rs1033214898
• NM_001080539.2:c.1327G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001080539.2(CCDC150):​c.1327G>T​(p.Ala443Ser) 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. 16/22 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. A443T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC150 NM_001080539.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986
• Publications: 0 publications found

Genes affected

CCDC150 (HGNC:26834): (coiled-coil domain containing 150)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.053969085).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC150	NM_001080539.2	c.1327G>T	p.Ala443Ser	missense_variant	Exon 12 of 28	ENST00000389175.9	NP_001074008.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC150	ENST00000389175.9	c.1327G>T	p.Ala443Ser	missense_variant	Exon 12 of 28	5	NM_001080539.2	ENSP00000373827.4
CCDC150	ENST00000431807.6	n.*473G>T		non_coding_transcript_exon_variant	Exon 8 of 23	2		ENSP00000389008.2
CCDC150	ENST00000497159.1	n.164G>T		non_coding_transcript_exon_variant	Exon 2 of 5	5
CCDC150	ENST00000431807.6	n.*473G>T		3_prime_UTR_variant	Exon 8 of 23	2		ENSP00000389008.2

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	0.081
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.62
DANN	Benign	0.28
DEOGEN2	Benign	0.0042	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.031	N
LIST_S2	Benign	0.43	T
M_CAP	Benign	0.0072	T
MetaRNN	Benign	0.054	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.7	L
PhyloP100		-0.99
PrimateAI	Benign	0.22	T
PROVEAN	Benign	-0.19	N
REVEL	Benign	0.014
Sift	Benign	0.45	T
Sift4G	Benign	0.38	T
Polyphen		0.0	B
Vest4		0.10
MutPred		0.080		Gain of phosphorylation at A443 (P = 0.0248);
MVP		0.014
MPC		0.032
ClinPred		0.021	T
GERP RS		-3.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.017
gMVP		0.023
Mutation Taster		=93/7	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

dbSNP: rs1033214898; hg19: chr2-197541342; COSMIC: COSV55876361; COSMIC: COSV55876361;