rs9383932

Variant names:

• chr6-151598585-A-G
• rs9383932
• NM_025059.4:c.1710+2008A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-151598585-A-G
• chr6-151598585-A-T

Variant summary

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

The NM_025059.4(CCDC170):​c.1710+2008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,116 control chromosomes in the GnomAD database, including 1,955 homozygotes. 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: 𝑓 0.15 (1955 hom., cov: 32)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1710+2008A>G		intron_variant	Intron 9 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1728+2008A>G		intron_variant	Intron 9 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1527+2008A>G		intron_variant	Intron 8 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1509+2008A>G		intron_variant	Intron 8 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1710+2008A>G		intron_variant	Intron 9 of 10	1	NM_025059.4	ENSP00000239374.6
CCDC170	ENST00000537358.1	n.496+2008A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23234 AN: 151998 Hom.: 1951 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.153 AC: 23272 AN: 152116 Hom.: 1955 Cov.: 32 AF XY: 0.154 AC XY: 11419 AN XY: 74364

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.169

Alfa AF: 0.133 Hom.: 1392

Bravo AF: 0.154

Asia WGS AF: 0.274 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.74
DANN	Benign	0.24

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: rs9383932; hg19: chr6-151919720;