9-15571694-C-G

Variant names:

• chr9-15571694-C-G
• rs771200123
• NM_173550.4:c.112C>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001348002.2(CCDC171):​c.-330C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,431,098 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: CCDC171 NM_001348002.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31789434).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348002.2. 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
	CCDC171	NM_173550.4	MANE Select	c.112C>G	p.Leu38Val	missense	Exon 3 of 26	NP_775821.2
	CCDC171	NM_001348002.2		c.-330C>G		5_prime_UTR_premature_start_codon_gain	Exon 3 of 27	NP_001334931.1
	CCDC171	NM_001355547.1		c.112C>G	p.Leu38Val	missense	Exon 2 of 25	NP_001342476.1	Q6TFL3-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC171	ENST00000380701.8	TSL:1 MANE Select	c.112C>G	p.Leu38Val	missense	Exon 3 of 26	ENSP00000370077.3	Q6TFL3-1
	CCDC171	ENST00000905141.1		c.112C>G	p.Leu38Val	missense	Exon 3 of 26	ENSP00000575200.1
	CCDC171	ENST00000971281.1		c.112C>G	p.Leu38Val	missense	Exon 3 of 26	ENSP00000641340.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000140 AC: 2 AN: 1431098 Hom.: 0 Cov.: 28 AF XY: 0.00000281 AC XY: 2 AN XY: 711988

African (AFR) AF: 0.00 AC: 0 AN: 31600

American (AMR) AF: 0.00 AC: 0 AN: 36472

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25518

East Asian (EAS) AF: 0.00 AC: 0 AN: 38034

South Asian (SAS) AF: 0.0000125 AC: 1 AN: 79758

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53238

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5698

European-Non Finnish (NFE) AF: 9.08e-7 AC: 1 AN: 1101706

Other (OTH) AF: 0.00 AC: 0 AN: 59074

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.048	T
Eigen	Uncertain	0.27
Eigen_PC	Uncertain	0.31
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.32	T
MetaSVM	Benign	-0.72	T
MutationAssessor	Benign	1.8	L
PhyloP100		1.7
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	-1.0	N
REVEL	Benign	0.055
Sift	Uncertain	0.0050	D
Sift4G	Benign	0.25	T
Polyphen		0.97	D
Vest4		0.47
MutPred		0.30		Gain of methylation at K40 (P = 0.0704)
MVP		0.15
ClinPred		0.92	D
GERP RS		4.5
Varity_R		0.20
gMVP		0.11
Mutation Taster		=94/6	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: rs771200123; hg19: chr9-15571692;