chr6-151618713-C-T

Variant names:

• chr6-151618713-C-T
• rs9383935
• NM_025059.4:c.*566C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_025059.4(CCDC170):​c.*566C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 155,362 control chromosomes in the GnomAD database, including 596 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (589 hom., cov: 32)
  • Exomes 𝑓: 0.054 (7 hom.)
• Consequence: CCDC170 NM_025059.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.303
• Publications: 17 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 6-151618713-C-T is Benign according to our data. Variant chr6-151618713-C-T is described in ClinVar as Benign. ClinVar VariationId is 1263708.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	NM_025059.4	MANE Select	c.*566C>T		3_prime_UTR	Exon 11 of 11	NP_079335.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC170	ENST00000239374.8	TSL:1 MANE Select	c.*566C>T		3_prime_UTR	Exon 11 of 11	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11064 AN: 152098 Hom.: 590 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.0962

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.0675

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0783

Gnomad OTH AF: 0.0918

GnomAD4 exome AF: 0.0537 AC: 169 AN: 3146 Hom.: 7 Cov.: 0 AF XY: 0.0560 AC XY: 92 AN XY: 1644

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.0419 AC: 39 AN: 930

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.273 AC: 12 AN: 44

South Asian (SAS) AF: 0.0679 AC: 19 AN: 280

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0529 AC: 94 AN: 1776

Other (OTH) AF: 0.0532 AC: 5 AN: 94

GnomAD4 genome AF: 0.0727 AC: 11062 AN: 152216 Hom.: 589 Cov.: 32 AF XY: 0.0714 AC XY: 5313 AN XY: 74424

African (AFR) AF: 0.0451 AC: 1874 AN: 41536

American (AMR) AF: 0.0708 AC: 1082 AN: 15290

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

East Asian (EAS) AF: 0.304 AC: 1575 AN: 5176

South Asian (SAS) AF: 0.0679 AC: 327 AN: 4814

European-Finnish (FIN) AF: 0.0265 AC: 281 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0782 AC: 5320 AN: 68000

Other (OTH) AF: 0.0922 AC: 195 AN: 2114

Alfa AF: 0.0791 Hom.: 688

Bravo AF: 0.0767

Asia WGS AF: 0.165 AC: 572 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Feb 17, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 25116933)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.5
DANN	Benign	0.56
PhyloP100		-0.30
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: rs9383935; hg19: chr6-151939848;