rs9830735

Variant summary

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

The ENST00000383794.7(CCDC174):​c.307+1199G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,182 control chromosomes in the GnomAD database, including 8,438 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 0.33 ( 8438 hom., cov: 33)

Consequence

CCDC174
ENST00000383794.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.45
Variant links:
Genes affected
CCDC174 (HGNC:28033): (coiled-coil domain containing 174) The protein encoded by this gene is found in the nucleus, where it interacts with eukaryotic translation initiation factor 4A, isoform 3. The encoded protein appears to be a part of the exon junction complex, which is involved in RNA processing, translation, and nonsense-mediated mRNA decay. A mutation in this gene has been associated with infantile hypotonia with psychomotor retardation. [provided by RefSeq, Mar 2016]

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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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CCDC174NM_016474.5 linkuse as main transcriptc.307+1199G>A intron_variant ENST00000383794.7 NP_057558.3
LOC124906215XR_007095827.1 linkuse as main transcriptn.427-938C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CCDC174ENST00000383794.7 linkuse as main transcriptc.307+1199G>A intron_variant 1 NM_016474.5 ENSP00000373304 P1
CCDC174ENST00000465759.1 linkuse as main transcriptn.371+1199G>A intron_variant, non_coding_transcript_variant 1
CCDC174ENST00000303688.8 linkuse as main transcriptc.307+1199G>A intron_variant 5 ENSP00000302344
CCDC174ENST00000463438.5 linkuse as main transcriptn.380+1199G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.330
AC:
50179
AN:
152064
Hom.:
8428
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.298
Gnomad AMI
AF:
0.387
Gnomad AMR
AF:
0.386
Gnomad ASJ
AF:
0.295
Gnomad EAS
AF:
0.246
Gnomad SAS
AF:
0.248
Gnomad FIN
AF:
0.424
Gnomad MID
AF:
0.256
Gnomad NFE
AF:
0.335
Gnomad OTH
AF:
0.346
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.330
AC:
50219
AN:
152182
Hom.:
8438
Cov.:
33
AF XY:
0.330
AC XY:
24579
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.298
Gnomad4 AMR
AF:
0.387
Gnomad4 ASJ
AF:
0.295
Gnomad4 EAS
AF:
0.246
Gnomad4 SAS
AF:
0.247
Gnomad4 FIN
AF:
0.424
Gnomad4 NFE
AF:
0.335
Gnomad4 OTH
AF:
0.347
Alfa
AF:
0.338
Hom.:
1075
Bravo
AF:
0.331
Asia WGS
AF:
0.264
AC:
914
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.23
DANN
Benign
0.69

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: rs9830735; hg19: chr3-14701635; API