chr1-42556139-C-T

Variant names:

• chr1-42556139-C-T
• rs12038786
• NM_001395517.1:c.891-17C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	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	c.891-17C>T		intron_variant	Intron 9 of 20		NM_001395517.1	ENSP00000499662.2

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

GnomAD2 exomes AF: 0.385 AC: 90716 AN: 235504 AF XY: 0.394

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 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

African (AFR) AF: 0.419 AC: 13435 AN: 32052

American (AMR) AF: 0.309 AC: 12531 AN: 40614

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 9571 AN: 25202

East Asian (EAS) AF: 0.536 AC: 21197 AN: 39568

South Asian (SAS) AF: 0.537 AC: 44535 AN: 82962

European-Finnish (FIN) AF: 0.250 AC: 13253 AN: 53014

Middle Eastern (MID) AF: 0.418 AC: 2362 AN: 5648

European-Non Finnish (NFE) AF: 0.363 AC: 401692 AN: 1105216

Other (OTH) AF: 0.398 AC: 23671 AN: 59470

GnomAD4 genome AF: 0.380 AC: 57686 AN: 151780 Hom.: 11449 Cov.: 32 AF XY: 0.379 AC XY: 28128 AN XY: 74154

African (AFR) AF: 0.416 AC: 17185 AN: 41322

American (AMR) AF: 0.338 AC: 5162 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3071 AN: 5182

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4820

European-Finnish (FIN) AF: 0.253 AC: 2658 AN: 10486

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24436 AN: 67926

Other (OTH) AF: 0.391 AC: 824 AN: 2110

Alfa AF: 0.368 Hom.: 2443

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
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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