Variant 22-30370709-G-A details in Genebe, Genetics Data Aggregator

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

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)

CCDC157 links:

KIAA1656 (HGNC:):

KIAA1656 links:

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]

RNF215 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

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

Synonymous conserved (PhyloP=-3.09 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 25 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC157	NM_001017437.5 linkuse as main transcript	c.804G>A	p.Pro268=	synonymous_variant	5/12	ENST00000338306.8	NP_001017437.3
KIAA1656	NR_046312.1 linkuse as main transcript	n.5707C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
CCDC157	ENST00000338306.8 linkuse as main transcript	c.804G>A	p.Pro268=	synonymous_variant	5/12	5	NM_001017437.5	ENSP00000343087	P1
CCDC157	ENST00000405659.5 linkuse as main transcript	c.804G>A	p.Pro268=	synonymous_variant	5/12	1		ENSP00000385357	P1
CCDC157	ENST00000475975.5 linkuse as main transcript	n.729G>A		non_coding_transcript_exon_variant	4/10	2
RNF215	ENST00000332468.5 linkuse as main transcript	c.*6066C>T		3_prime_UTR_variant, NMD_transcript_variant	3/3	5		ENSP00000487588

Frequencies

GnomAD3 genomes

AF:

0.00322

AC:

491

AN:

152250

Hom.:

Cov.:

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.:

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.:

Cov.:

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

AF:

0.00322

AC:

490

AN:

152368

Hom.:

Cov.:

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.:

Bravo

AF:

0.00353

Asia WGS

AF:

0.000289

AC:

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

CCDC157: 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over