Genetic Variant CCDC73:p.Val959Gly (chr11-32613442-A-C) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The NM_001008391.4(CCDC73):c.2876T>G(p.Val959Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00305 in 1,611,548 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0031 ( 14 hom. )

Consequence

CCDC73
NM_001008391.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.22

Variant links:

Genes affected

CCDC73 (HGNC:23261): (coiled-coil domain containing 73)

CCDC73 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=0.0032474399).

BP6

Variant 11-32613442-A-C is Benign according to our data. Variant chr11-32613442-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2641706.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 14 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC73	NM_001008391.4 link	c.2876T>G	p.Val959Gly	missense_variant	Exon 16 of 18	ENST00000335185.10	NP_001008392.2	Q6ZRK6-1
CCDC73	XM_047427029.1 link	c.2876T>G	p.Val959Gly	missense_variant	Exon 21 of 23		XP_047282985.1
CCDC73	XM_047427030.1 link	c.2876T>G	p.Val959Gly	missense_variant	Exon 16 of 18		XP_047282986.1
CCDC73	XM_047427031.1 link	c.2618T>G	p.Val873Gly	missense_variant	Exon 15 of 17		XP_047282987.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC73	ENST00000335185.10 link	c.2876T>G	p.Val959Gly	missense_variant	Exon 16 of 18	2	NM_001008391.4	ENSP00000335325.5		Q6ZRK6-1
CCDC73	ENST00000528333.1 link	c.136-10422T>G		intron_variant	Intron 1 of 1	3		ENSP00000434365.1		H0YDV2

Frequencies

GnomAD3 genomes

AF:

0.00256

AC:

390

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000772

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00504

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00849

Gnomad FIN

AF:

0.000376

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00328

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00260

AC:

647

AN:

248466

Hom.:

AF XY:

0.00299

AC XY:

403

AN XY:

134804

show subpopulations

Gnomad AFR exome

AF:

0.000581

Gnomad AMR exome

AF:

0.00193

Gnomad ASJ exome

AF:

0.000100

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00720

Gnomad FIN exome

AF:

0.000465

Gnomad NFE exome

AF:

0.00283

Gnomad OTH exome

AF:

0.00365

GnomAD4 exome

AF:

0.00310

AC:

4530

AN:

1459220

Hom.:

Cov.:

AF XY:

0.00328

AC XY:

2377

AN XY:

725496

show subpopulations

Gnomad4 AFR exome

AF:

0.000569

Gnomad4 AMR exome

AF:

0.00205

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00720

Gnomad4 FIN exome

AF:

0.000300

Gnomad4 NFE exome

AF:

0.00320

Gnomad4 OTH exome

AF:

0.00299

GnomAD4 genome

AF:

0.00256

AC:

390

AN:

152328

Hom.:

Cov.:

AF XY:

0.00240

AC XY:

179

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.000770

Gnomad4 AMR

AF:

0.00503

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00850

Gnomad4 FIN

AF:

0.000376

Gnomad4 NFE

AF:

0.00328

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00173

Hom.:

Bravo

AF:

0.00269

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00311

AC:

ESP6500AA

AF:

0.000825

AC:

ESP6500EA

AF:

0.00319

AC:

ExAC

AF:

0.00270

AC:

326

Asia WGS

AF:

0.00318

AC:

AN:

3478

EpiCase

AF:

0.00333

EpiControl

AF:

0.00373

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CCDC73: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.60

CADD

Benign

0.031

DANN

Benign

0.60

DEOGEN2

Benign

0.0071

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.050

LIST_S2

Benign

0.16

MetaRNN

Benign

0.0032

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.49

PrimateAI

Benign

0.25

PROVEAN

Benign

-0.90

REVEL

Benign

0.030

Sift

Benign

0.16

Sift4G

Benign

0.086

Polyphen

0.0010

Vest4

0.11

MVP

0.17

MPC

0.15

ClinPred

0.0059

GERP RS

-11

Varity_R

0.054

gMVP

0.087

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