rs2809658

Variant names:

• chr1-42584725-G-A
• rs2809658
• NM_001395517.1:c.1685+3211G>A

Variant summary

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

The NM_001395517.1(CCDC30):​c.1685+3211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,058 control chromosomes in the GnomAD database, including 27,980 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 0.60 (27980 hom., cov: 33)
• Consequence: CCDC30 NM_001395517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 4 publications found

Genes affected

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

ENSG00000285728 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC30	NM_001395517.1	c.1685+3211G>A		intron_variant	Intron 13 of 20	ENST00000657597.2	NP_001382446.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC30	ENST00000657597.2	c.1685+3211G>A		intron_variant	Intron 13 of 20		NM_001395517.1	ENSP00000499662.2

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91372 AN: 151942 Hom.: 27953 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.588

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.601 AC: 91454 AN: 152058 Hom.: 27980 Cov.: 33 AF XY: 0.604 AC XY: 44858 AN XY: 74326

African (AFR) AF: 0.686 AC: 28466 AN: 41498

American (AMR) AF: 0.579 AC: 8845 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1838 AN: 3468

East Asian (EAS) AF: 0.814 AC: 4210 AN: 5174

South Asian (SAS) AF: 0.711 AC: 3422 AN: 4812

European-Finnish (FIN) AF: 0.491 AC: 5170 AN: 10540

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37385 AN: 67974

Other (OTH) AF: 0.591 AC: 1248 AN: 2112

Alfa AF: 0.564 Hom.: 78175

Bravo AF: 0.606

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.8
DANN	Benign	0.66
PhyloP100		-0.64
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: rs2809658; hg19: chr1-43050396;