9-15784633-A-T

Variant names:

• chr9-15784633-A-T
• rs1539172
• NM_173550.4:c.3206A>T

Variant summary

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

The NM_173550.4(CCDC171):​c.3206A>T​(p.Lys1069Ile) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC171 NM_173550.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44
• Publications: 41 publications found

Genes affected

CCDC171 (HGNC:29828): (coiled-coil domain containing 171)

LOC107987049 (HGNC:):

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=0.15858969).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC171	NM_173550.4	c.3206A>T	p.Lys1069Ile	missense_variant	Exon 21 of 26	ENST00000380701.8	NP_775821.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC171	ENST00000380701.8	c.3206A>T	p.Lys1069Ile	missense_variant	Exon 21 of 26	1	NM_173550.4	ENSP00000370077.3
CCDC171	ENST00000449575.6	c.923A>T	p.Lys308Ile	missense_variant	Exon 5 of 11	2		ENSP00000409055.2
CCDC171	ENST00000432954.1	c.365A>T	p.Lys122Ile	missense_variant	Exon 3 of 6	2		ENSP00000399526.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.47
BayesDel_addAF	Benign	0.0073	T
BayesDel_noAF	Benign	-0.23
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.069	T
Eigen	Benign	-0.069
Eigen_PC	Benign	0.024
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.28	T
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.16	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	1.7	L
PhyloP100		3.4
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-2.3	N
REVEL	Benign	0.26
Sift	Uncertain	0.0060	D
Sift4G	Uncertain	0.021	D
Polyphen		0.23	B
Vest4		0.36
MutPred		0.31		Gain of loop (P = 0.0013);
MVP		0.34
ClinPred		0.91	D
GERP RS		4.1
Varity_R		0.23
gMVP		0.27
Mutation Taster		=86/14	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: rs1539172; hg19: chr9-15784631;