Menu
GeneBe

22-30370709-G-A

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001017437.5(CCDC157):c.804G>A(p.Pro268=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 1,613,370 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0052 ( 25 hom. )

Consequence

CCDC157
NM_001017437.5 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.09
Variant links:
Genes affected
CCDC157 (HGNC:33854): (coiled-coil domain containing 157)
RNF215 (HGNC:33434): (ring finger protein 215) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in Golgi to vacuole transport; protein targeting to vacuole; and ubiquitin-dependent protein catabolic process. Predicted to be integral component of membrane. Predicted to be part of Golgi transport complex. Predicted to be active in endosome; membrane; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 22-30370709-G-A is Benign according to our data. Variant chr22-30370709-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653057.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.09 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CCDC157NM_001017437.5 linkuse as main transcriptc.804G>A p.Pro268= synonymous_variant 5/12 ENST00000338306.8
KIAA1656NR_046312.1 linkuse as main transcriptn.5707C>T non_coding_transcript_exon_variant 2/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CCDC157ENST00000338306.8 linkuse as main transcriptc.804G>A p.Pro268= synonymous_variant 5/125 NM_001017437.5 P1
CCDC157ENST00000405659.5 linkuse as main transcriptc.804G>A p.Pro268= synonymous_variant 5/121 P1
CCDC157ENST00000475975.5 linkuse as main transcriptn.729G>A non_coding_transcript_exon_variant 4/102
RNF215ENST00000332468.5 linkuse as main transcriptc.*6066C>T 3_prime_UTR_variant, NMD_transcript_variant 3/35

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00322
AC:
491
AN:
152250
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000844
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00373
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00186
Gnomad FIN
AF:
0.00179
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00526
Gnomad OTH
AF:
0.00430
GnomAD3 exomes
AF:
0.00413
AC:
1026
AN:
248692
Hom.:
3
AF XY:
0.00414
AC XY:
559
AN XY:
134916
show subpopulations
Gnomad AFR exome
AF:
0.000628
Gnomad AMR exome
AF:
0.00264
Gnomad ASJ exome
AF:
0.000601
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00206
Gnomad FIN exome
AF:
0.00257
Gnomad NFE exome
AF:
0.00688
Gnomad OTH exome
AF:
0.00512
GnomAD4 exome
AF:
0.00523
AC:
7643
AN:
1461002
Hom.:
25
Cov.:
31
AF XY:
0.00511
AC XY:
3716
AN XY:
726806
show subpopulations
Gnomad4 AFR exome
AF:
0.000986
Gnomad4 AMR exome
AF:
0.00304
Gnomad4 ASJ exome
AF:
0.000689
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00235
Gnomad4 FIN exome
AF:
0.00219
Gnomad4 NFE exome
AF:
0.00616
Gnomad4 OTH exome
AF:
0.00459
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00322
AC:
490
AN:
152368
Hom.:
0
Cov.:
33
AF XY:
0.00303
AC XY:
226
AN XY:
74506
show subpopulations
Gnomad4 AFR
AF:
0.000842
Gnomad4 AMR
AF:
0.00372
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00186
Gnomad4 FIN
AF:
0.00179
Gnomad4 NFE
AF:
0.00526
Gnomad4 OTH
AF:
0.00425
Alfa
AF:
0.00431
Hom.:
1
Bravo
AF:
0.00353
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.00556
EpiControl
AF:
0.00534

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2023CCDC157: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
0.0030
Dann
Benign
0.82

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: rs141091935; hg19: chr22-30766698; API