rs9383589

Variant names:

• chr6-151619125-A-G
• rs9383589
• NM_025059.4:c.*978A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025059.4(CCDC170):​c.*978A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 152,188 control chromosomes in the GnomAD database, including 569 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency:
  • Genomes: 𝑓 0.070 (569 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: CCDC170 NM_025059.4 3_prime_UTR
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 0.188

Genes affected

CCDC170 (HGNC:21177): (coiled-coil domain containing 170) The function of this gene and its encoded protein is not known. Several genome-wide association studies have implicated the region around this gene to be involved in breast cancer and bone mineral density, but no link to this specific gene has been found. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.*978A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.*978A>G		3_prime_UTR_variant	Exon 11 of 11		XP_011534449.1
CCDC170	XM_011536148.3	c.*978A>G		3_prime_UTR_variant	Exon 10 of 10		XP_011534450.1
CCDC170	XM_047419372.1	c.*978A>G		3_prime_UTR_variant	Exon 10 of 10		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.*978A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10620 AN: 152062 Hom.: 570 Cov.: 32

Gnomad AFR AF: 0.0351

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0702

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0912

GnomAD4 exome AF: 0.125 AC: 1 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0698 AC: 10618 AN: 152180 Hom.: 569 Cov.: 32 AF XY: 0.0688 AC XY: 5119 AN XY: 74416

Gnomad4 AFR AF: 0.0351

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.0673

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0781

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0808 Hom.: 627

Bravo AF: 0.0730

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Estrogen resistance syndrome Uncertain:1

Mar 01, 2014

Department of Breast and Endocrine Surgery, Kumamoto University

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.67
DANN	Benign	0.80

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

LitVar

Other links and lift over

dbSNP: rs9383589; hg19: chr6-151940260;