NM_025059.4:c.1092+3880C>T

Variant names:

• chr6-151577371-C-T
• rs1871859
• NM_025059.4:c.1092+3880C>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.1092+3880C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,056 control chromosomes in the GnomAD database, including 3,121 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 0.18 (3121 hom., cov: 32)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 25 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1092+3880C>T		intron_variant	Intron 6 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1110+3880C>T		intron_variant	Intron 6 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1110+3880C>T		intron_variant	Intron 6 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1092+3880C>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.1092+3880C>T		intron_variant	Intron 6 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27969 AN: 151936 Hom.: 3120 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.184 AC: 28005 AN: 152056 Hom.: 3121 Cov.: 32 AF XY: 0.194 AC XY: 14432 AN XY: 74308

African (AFR) AF: 0.192 AC: 7971 AN: 41492

American (AMR) AF: 0.259 AC: 3962 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 661 AN: 3464

East Asian (EAS) AF: 0.529 AC: 2724 AN: 5150

South Asian (SAS) AF: 0.251 AC: 1212 AN: 4822

European-Finnish (FIN) AF: 0.206 AC: 2176 AN: 10550

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8591 AN: 67994

Other (OTH) AF: 0.193 AC: 407 AN: 2106

Alfa AF: 0.149 Hom.: 7236

Bravo AF: 0.191

Asia WGS AF: 0.384 AC: 1336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.42
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: rs1871859; hg19: chr6-151898506;