6-151580667-A-T

Variant names:

• chr6-151580667-A-T
• rs4869739
• NM_025059.4:c.1093-5222A>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.1093-5222A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,976 control chromosomes in the GnomAD database, including 17,273 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 0.44 (17273 hom., cov: 31)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 21 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 (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1093-5222A>T		intron_variant	Intron 6 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1111-5222A>T		intron_variant	Intron 6 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1110+7176A>T		intron_variant	Intron 6 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1092+7176A>T		intron_variant	Intron 6 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1093-5222A>T		intron_variant	Intron 6 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66532 AN: 151858 Hom.: 17237 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.438 AC: 66630 AN: 151976 Hom.: 17273 Cov.: 31 AF XY: 0.444 AC XY: 32981 AN XY: 74262

African (AFR) AF: 0.690 AC: 28599 AN: 41456

American (AMR) AF: 0.433 AC: 6615 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4203 AN: 5150

South Asian (SAS) AF: 0.455 AC: 2193 AN: 4822

European-Finnish (FIN) AF: 0.298 AC: 3146 AN: 10558

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19266 AN: 67940

Other (OTH) AF: 0.444 AC: 937 AN: 2112

Alfa AF: 0.207 Hom.: 423

Bravo AF: 0.460

Asia WGS AF: 0.643 AC: 2235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.54
PhyloP100		0.61
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: rs4869739; hg19: chr6-151901802;