6-151547655-C-T

Variant names:

• chr6-151547655-C-T
• rs9383922
• NM_025059.4:c.589-649C>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.589-649C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,886 control chromosomes in the GnomAD database, including 30,413 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 0.61 (30413 hom., cov: 30)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.589-649C>T		intron_variant	Intron 4 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.607-649C>T		intron_variant	Intron 4 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.607-649C>T		intron_variant	Intron 4 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.589-649C>T		intron_variant	Intron 4 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.589-649C>T		intron_variant	Intron 4 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92348 AN: 151768 Hom.: 30409 Cov.: 30

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.608 AC: 92372 AN: 151886 Hom.: 30413 Cov.: 30 AF XY: 0.614 AC XY: 45567 AN XY: 74216

African (AFR) AF: 0.338 AC: 14002 AN: 41372

American (AMR) AF: 0.724 AC: 11058 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2235 AN: 3466

East Asian (EAS) AF: 0.672 AC: 3454 AN: 5138

South Asian (SAS) AF: 0.682 AC: 3277 AN: 4802

European-Finnish (FIN) AF: 0.787 AC: 8316 AN: 10570

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47797 AN: 67944

Other (OTH) AF: 0.614 AC: 1297 AN: 2112

Alfa AF: 0.672 Hom.: 17488

Bravo AF: 0.595

Asia WGS AF: 0.658 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.67
PhyloP100		-3.0
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: rs9383922; hg19: chr6-151868790;