rs3734805

Variant names:

• chr6-151618215-A-C
• rs3734805
• NM_025059.4:c.*68A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-151618215-A-C
• chr6-151618215-A-G
• chr6-151618215-A-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.*68A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 1,341,036 control chromosomes in the GnomAD database, including 5,350 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 0.073 (588 hom., cov: 32)
  • Exomes 𝑓: 0.079 (4762 hom.)
• Consequence: CCDC170 NM_025059.4 3_prime_UTR
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: -0.00500
• Publications: 58 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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.*68A>C		3_prime_UTR	Exon 11 of 11	NP_079335.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.*68A>C		3_prime_UTR	Exon 11 of 11	ENSP00000239374.6	Q8IYT3
	CCDC170	ENST00000867015.1		c.*68A>C		3_prime_UTR	Exon 11 of 11	ENSP00000537074.1
	CCDC170	ENST00000867016.1		c.*68A>C		3_prime_UTR	Exon 10 of 10	ENSP00000537075.1

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11060 AN: 152116 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.0450

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0924

GnomAD4 exome AF: 0.0794 AC: 94405 AN: 1188802 Hom.: 4762 Cov.: 15 AF XY: 0.0791 AC XY: 47217 AN XY: 596630

African (AFR) AF: 0.0433 AC: 1191 AN: 27494

American (AMR) AF: 0.0526 AC: 2103 AN: 39988

Ashkenazi Jewish (ASJ) AF: 0.0969 AC: 2168 AN: 22378

East Asian (EAS) AF: 0.265 AC: 10031 AN: 37892

South Asian (SAS) AF: 0.0600 AC: 4497 AN: 74940

European-Finnish (FIN) AF: 0.0312 AC: 1618 AN: 51846

Middle Eastern (MID) AF: 0.107 AC: 406 AN: 3778

European-Non Finnish (NFE) AF: 0.0771 AC: 67820 AN: 879648

Other (OTH) AF: 0.0899 AC: 4571 AN: 50838

GnomAD4 genome AF: 0.0726 AC: 11058 AN: 152234 Hom.: 588 Cov.: 32 AF XY: 0.0714 AC XY: 5313 AN XY: 74424

African (AFR) AF: 0.0450 AC: 1870 AN: 41550

American (AMR) AF: 0.0708 AC: 1083 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0962 AC: 334 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1577 AN: 5168

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4826

European-Finnish (FIN) AF: 0.0263 AC: 279 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0782 AC: 5318 AN: 68014

Other (OTH) AF: 0.0929 AC: 196 AN: 2110

Alfa AF: 0.0828 Hom.: 3014

Bravo AF: 0.0767

Asia WGS AF: 0.165 AC: 571 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Estrogen resistance syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.39
DANN	Benign	0.51
PhyloP100		-0.0050
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: rs3734805; hg19: chr6-151939350; COSMIC: COSV53337016; COSMIC: COSV53337016;