dbSNP rs12038786: CCDC30:c.891-17C>T (chr1-42556139-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001395517.1(CCDC30):c.891-17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,595,526 control chromosomes in the GnomAD database, including 116,354 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 0.38 ( 11449 hom., cov: 32)

Exomes 𝑓: 0.38 ( 104905 hom. )

Consequence

CCDC30
NM_001395517.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.259

Variant links:

Genes affected

CCDC30 (HGNC:26103): (coiled-coil domain containing 30)

CCDC30 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC30	NM_001395517.1 link	c.891-17C>T		intron_variant	Intron 9 of 20	ENST00000657597.2	NP_001382446.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC30	ENST00000657597.2 link	c.891-17C>T		intron_variant	Intron 9 of 20		NM_001395517.1	ENSP00000499662.2		A0A590UK19

Frequencies

GnomAD3 genomes

AF:

0.380

AC:

57625

AN:

151664

Hom.:

11435

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.381

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.541

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.360

Gnomad OTH

AF:

0.386

GnomAD3 exomes

AF:

0.385

AC:

90716

AN:

235504

Hom.:

18596

AF XY:

0.394

AC XY:

50458

AN XY:

127906

show subpopulations

Gnomad AFR exome

AF:

0.417

Gnomad AMR exome

AF:

0.305

Gnomad ASJ exome

AF:

0.382

Gnomad EAS exome

AF:

0.611

Gnomad SAS exome

AF:

0.543

Gnomad FIN exome

AF:

0.241

Gnomad NFE exome

AF:

0.357

Gnomad OTH exome

AF:

0.369

GnomAD4 exome

AF:

0.376

AC:

542247

AN:

1443746

Hom.:

104905

Cov.:

AF XY:

0.380

AC XY:

272978

AN XY:

718088

show subpopulations

Gnomad4 AFR exome

AF:

0.419

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.380

Gnomad4 EAS exome

AF:

0.536

Gnomad4 SAS exome

AF:

0.537

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.398

GnomAD4 genome

AF:

0.380

AC:

57686

AN:

151780

Hom.:

11449

Cov.:

AF XY:

0.379

AC XY:

28128

AN XY:

74154

show subpopulations

Gnomad4 AFR

AF:

0.416

Gnomad4 AMR

AF:

0.338

Gnomad4 ASJ

AF:

0.381

Gnomad4 EAS

AF:

0.593

Gnomad4 SAS

AF:

0.540

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.360

Gnomad4 OTH

AF:

0.391

Alfa

AF:

0.368

Hom.:

2381

Bravo

AF:

0.388

Asia WGS

AF:

0.581

AC:

2020

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.8

DANN

Benign

0.50

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over