chr6-151604242-C-T

Variant names:

• chr6-151604242-C-T
• rs900195
• NM_025059.4:c.1710+7665C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025059.4(CCDC170):​c.1710+7665C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,978 control chromosomes in the GnomAD database, including 21,066 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 0.49 (21066 hom., cov: 31)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	NM_025059.4	MANE Select	c.1710+7665C>T		intron	N/A	NP_079335.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.1710+7665C>T		intron	N/A	ENSP00000239374.6	Q8IYT3
	CCDC170	ENST00000867015.1		c.1689+7665C>T		intron	N/A	ENSP00000537074.1
	CCDC170	ENST00000867016.1		c.1581+7665C>T		intron	N/A	ENSP00000537075.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74123 AN: 151860 Hom.: 21066 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.488 AC: 74154 AN: 151978 Hom.: 21066 Cov.: 31 AF XY: 0.486 AC XY: 36120 AN XY: 74284

African (AFR) AF: 0.197 AC: 8184 AN: 41466

American (AMR) AF: 0.481 AC: 7348 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2013 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1268 AN: 5154

South Asian (SAS) AF: 0.568 AC: 2735 AN: 4814

European-Finnish (FIN) AF: 0.662 AC: 6983 AN: 10542

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43839 AN: 67952

Other (OTH) AF: 0.491 AC: 1036 AN: 2110

Alfa AF: 0.608 Hom.: 24650

Bravo AF: 0.460

Asia WGS AF: 0.373 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.40
DANN	Benign	0.58
PhyloP100		-1.5
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: rs900195; hg19: chr6-151925377;