rs12038786

chr1-42556139-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395517.1(CCDC30):c.891-17C>T variant causes a splice polypyrimidine tract, 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 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

Genes affected

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

ACMG classification

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/exons	MANE	UniProt
CCDC30	NM_001395517.1	c.891-17C>T		splice_polypyrimidine_tract_variant, intron_variant		ENST00000657597.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC30	ENST00000657597.2	c.891-17C>T		splice_polypyrimidine_tract_variant, intron_variant			NM_001395517.1	A2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57625 AN: 151664 Hom.: 11435 Cov.: 32

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

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.: 32 AF XY: 0.380 AC XY: 272978 AN XY: 718088

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.: 32 AF XY: 0.379 AC XY: 28128 AN XY: 74154

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

Other links and lift over

dbSNP: rs12038786; hg19: chr1-43021810; COSMIC: COSV59606794;