rs1038304

Positions:

• chr6-151612040-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC107986528 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC170	NM_025059.4	c.1711-3403A>G		intron_variant		ENST00000239374.8
LOC107986528	XR_001743865.2	n.106-768T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC170	ENST00000239374.8	c.1711-3403A>G		intron_variant		1	NM_025059.4	P1
CCDC170	ENST00000537358.1	n.497-3403A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.453

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.596

Alfa AF: 0.523 Hom.: 41990

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1038304; hg19: chr6-151933175;