rs9478223

Positions:

• chr6-151579103-T-C
• chr6-151579103-T-G

Variant summary

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

The NM_025059.4(CCDC170):​c.1092+5612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,864 control chromosomes in the GnomAD database, including 2,071 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 (2071 hom., cov: 32)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1092+5612T>C		intron_variant		ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1110+5612T>C		intron_variant			XP_011534449.1
CCDC170	XM_011536148.3	c.1110+5612T>C		intron_variant			XP_011534450.1
CCDC170	XM_047419372.1	c.1092+5612T>C		intron_variant			XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1092+5612T>C		intron_variant		1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22600 AN: 151746 Hom.: 2066 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.0692

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0708

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.149 AC: 22640 AN: 151864 Hom.: 2071 Cov.: 32 AF XY: 0.145 AC XY: 10782 AN XY: 74208

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.0688

Gnomad4 SAS AF: 0.0729

Gnomad4 FIN AF: 0.0708

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.151

Alfa AF: 0.107 Hom.: 1161

Bravo AF: 0.158

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.57

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: rs9478223; hg19: chr6-151900238;