6-151579103-T-C

Variant names:

• chr6-151579103-T-C
• rs9478223
• NM_025059.4:c.1092+5612T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025059.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	NM_025059.4	MANE Select	c.1092+5612T>C		intron	N/A	NP_079335.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.1092+5612T>C		intron	N/A	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

African (AFR) AF: 0.270 AC: 11157 AN: 41326

American (AMR) AF: 0.129 AC: 1963 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3468

East Asian (EAS) AF: 0.0688 AC: 356 AN: 5178

South Asian (SAS) AF: 0.0729 AC: 351 AN: 4814

European-Finnish (FIN) AF: 0.0708 AC: 747 AN: 10554

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7377 AN: 67956

Other (OTH) AF: 0.151 AC: 317 AN: 2106

Alfa AF: 0.115 Hom.: 1738

Bravo AF: 0.158

Asia WGS AF: 0.0920 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.58
DANN	Benign	0.57
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs9478223; hg19: chr6-151900238;