rs9478223

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000239374.8(CCDC170):​c.1092+5612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 151,864 control chromosomes in the GnomAD database, including 2,071 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 0.15 ( 2071 hom., cov: 32)

Consequence

CCDC170
ENST00000239374.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC170NM_025059.4 linkuse as main transcriptc.1092+5612T>C intron_variant ENST00000239374.8 NP_079335.2
CCDC170XM_011536147.3 linkuse as main transcriptc.1110+5612T>C intron_variant XP_011534449.1
CCDC170XM_011536148.3 linkuse as main transcriptc.1110+5612T>C intron_variant XP_011534450.1
CCDC170XM_047419372.1 linkuse as main transcriptc.1092+5612T>C intron_variant XP_047275328.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC170ENST00000239374.8 linkuse as main transcriptc.1092+5612T>C intron_variant 1 NM_025059.4 ENSP00000239374 P1

Frequencies

GnomAD3 genomes
AF:
0.149
AC:
22600
AN:
151746
Hom.:
2066
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.270
Gnomad AMI
AF:
0.0407
Gnomad AMR
AF:
0.129
Gnomad ASJ
AF:
0.0903
Gnomad EAS
AF:
0.0692
Gnomad SAS
AF:
0.0731
Gnomad FIN
AF:
0.0708
Gnomad MID
AF:
0.0759
Gnomad NFE
AF:
0.109
Gnomad OTH
AF:
0.149
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.149
AC:
22640
AN:
151864
Hom.:
2071
Cov.:
32
AF XY:
0.145
AC XY:
10782
AN XY:
74208
show subpopulations
Gnomad4 AFR
AF:
0.270
Gnomad4 AMR
AF:
0.129
Gnomad4 ASJ
AF:
0.0903
Gnomad4 EAS
AF:
0.0688
Gnomad4 SAS
AF:
0.0729
Gnomad4 FIN
AF:
0.0708
Gnomad4 NFE
AF:
0.109
Gnomad4 OTH
AF:
0.151
Alfa
AF:
0.107
Hom.:
1161
Bravo
AF:
0.158
Asia WGS
AF:
0.0920
AC:
321
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.58
DANN
Benign
0.57

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9478223; hg19: chr6-151900238; API