dbSNP rs76597070: CCDC27:p.Arg104Lys (chr1-3752792-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_152492.3(CCDC27):c.311G>A(p.Arg104Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00949 in 1,611,598 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0098 ( 78 hom. )

Consequence

CCDC27
NM_152492.3 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.145

Variant links:

Genes affected

CCDC27 (HGNC:26546): (coiled-coil domain containing 27)

CCDC27 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003395021).

BP6

Variant 1-3752792-G-A is Benign according to our data. Variant chr1-3752792-G-A is described in ClinVar as [Benign]. Clinvar id is 788937.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC27	NM_152492.3 link	c.311G>A	p.Arg104Lys	missense_variant	Exon 1 of 12	ENST00000294600.7	NP_689705.2	Q2M243

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCDC27	ENST00000294600.7 link	c.311G>A	p.Arg104Lys	missense_variant	Exon 1 of 12	1	NM_152492.3	ENSP00000294600.2	Q2M243
CCDC27	ENST00000462521.2 link	n.311G>A		non_coding_transcript_exon_variant	Exon 1 of 12	5		ENSP00000463275.1	J3QKX2
CCDC27	ENST00000636250.1 link	n.821G>A		non_coding_transcript_exon_variant	Exon 4 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.00636

AC:

968

AN:

152228

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00504

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00311

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0111

Gnomad OTH

AF:

0.00766

GnomAD3 exomes

AF:

0.00636

AC:

1582

AN:

248854

Hom.:

AF XY:

0.00677

AC XY:

914

AN XY:

134978

show subpopulations

Gnomad AFR exome

AF:

0.00126

Gnomad AMR exome

AF:

0.00279

Gnomad ASJ exome

AF:

0.00210

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00350

Gnomad FIN exome

AF:

0.00354

Gnomad NFE exome

AF:

0.0109

Gnomad OTH exome

AF:

0.00727

GnomAD4 exome

AF:

0.00982

AC:

14326

AN:

1459252

Hom.:

Cov.:

AF XY:

0.00966

AC XY:

7009

AN XY:

725532

show subpopulations

Gnomad4 AFR exome

AF:

0.00120

Gnomad4 AMR exome

AF:

0.00327

Gnomad4 ASJ exome

AF:

0.00184

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00387

Gnomad4 FIN exome

AF:

0.00412

Gnomad4 NFE exome

AF:

0.0118

Gnomad4 OTH exome

AF:

0.00743

GnomAD4 genome

AF:

0.00635

AC:

967

AN:

152346

Hom.:

Cov.:

AF XY:

0.00599

AC XY:

446

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00168

Gnomad4 AMR

AF:

0.00503

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00311

Gnomad4 NFE

AF:

0.0111

Gnomad4 OTH

AF:

0.00758

Alfa

AF:

0.00950

Hom.:

Bravo

AF:

0.00672

TwinsUK

AF:

0.00917

AC:

ALSPAC

AF:

0.0114

AC:

ESP6500AA

AF:

0.00159

AC:

ESP6500EA

AF:

0.0102

AC:

ExAC

AF:

0.00677

AC:

822

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.0103

EpiControl

AF:

0.00914

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 04, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.70

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.6

DANN

Benign

0.66

DEOGEN2

Benign

0.0051

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.014

LIST_S2

Benign

0.29

MetaRNN

Benign

0.0034

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.63

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.46

REVEL

Benign

0.018

Sift

Benign

0.38

Sift4G

Benign

0.42

Polyphen

0.0070

Vest4

0.076

MVP

0.072

MPC

0.35

ClinPred

0.0013

GERP RS

-0.27

Varity_R

0.042

gMVP

0.053

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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