NM_025059.4:c.1710+1144T>G

Variant names:

• chr6-151597721-T-G
• rs12662670
• NM_025059.4:c.1710+1144T>G

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+1144T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 152,230 control chromosomes in the GnomAD database, including 563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: 𝑓 0.072 (563 hom., cov: 33)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.126
• Publications: 55 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1710+1144T>G		intron_variant	Intron 9 of 10	ENST00000239374.8	NP_079335.2
CCDC170	XM_011536147.3	c.1728+1144T>G		intron_variant	Intron 9 of 10		XP_011534449.1
CCDC170	XM_011536148.3	c.1527+1144T>G		intron_variant	Intron 8 of 9		XP_011534450.1
CCDC170	XM_047419372.1	c.1509+1144T>G		intron_variant	Intron 8 of 9		XP_047275328.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1710+1144T>G		intron_variant	Intron 9 of 10	1	NM_025059.4	ENSP00000239374.6
CCDC170	ENST00000537358.1	n.496+1144T>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 11001 AN: 152112 Hom.: 562 Cov.: 33

Gnomad AFR AF: 0.0459

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0889

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.0700

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.0723 AC: 11008 AN: 152230 Hom.: 563 Cov.: 33 AF XY: 0.0715 AC XY: 5325 AN XY: 74434

African (AFR) AF: 0.0460 AC: 1912 AN: 41530

American (AMR) AF: 0.0699 AC: 1069 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0889 AC: 308 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1539 AN: 5164

South Asian (SAS) AF: 0.0707 AC: 341 AN: 4826

European-Finnish (FIN) AF: 0.0310 AC: 329 AN: 10618

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0771 AC: 5242 AN: 68012

Other (OTH) AF: 0.0951 AC: 201 AN: 2114

Alfa AF: 0.0745 Hom.: 632

Bravo AF: 0.0757

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Estrogen resistance syndrome Uncertain:1

Mar 01, 2014

Department of Breast and Endocrine Surgery, Kumamoto University

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.5
DANN	Benign	0.62
PhyloP100		-0.13
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: rs12662670; hg19: chr6-151918856;