NM_025059.4:c.1711-3403A>G

Variant names:

• chr6-151612040-A-G
• rs1038304
• NM_025059.4:c.1711-3403A>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.1711-3403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,030 control chromosomes in the GnomAD database, including 26,985 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 0.58 (26985 hom., cov: 32)
• Consequence: CCDC170 NM_025059.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 64 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]

ENSG00000300966 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC170	NM_025059.4	c.1711-3403A>G		intron_variant	Intron 9 of 10	ENST00000239374.8	NP_079335.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC170	ENST00000239374.8	c.1711-3403A>G		intron_variant	Intron 9 of 10	1	NM_025059.4	ENSP00000239374.6

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87647 AN: 151912 Hom.: 26947 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.577 AC: 87725 AN: 152030 Hom.: 26985 Cov.: 32 AF XY: 0.569 AC XY: 42315 AN XY: 74318

African (AFR) AF: 0.805 AC: 33384 AN: 41466

American (AMR) AF: 0.453 AC: 6912 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1961 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2545 AN: 5166

South Asian (SAS) AF: 0.524 AC: 2527 AN: 4820

European-Finnish (FIN) AF: 0.406 AC: 4287 AN: 10564

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34290 AN: 67966

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.533 Hom.: 66469

Bravo AF: 0.591

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.85
DANN	Benign	0.70
PhyloP100		-0.40
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: rs1038304; hg19: chr6-151933175;