rs2809658

chr1-42584725-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC124904162 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC30	NM_001395517.1	c.1685+3211G>A		intron_variant		ENST00000657597.2
LOC124904162	XR_007066034.1	n.77-13565C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC30	ENST00000657597.2	c.1685+3211G>A		intron_variant			NM_001395517.1	A2

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

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.591

Alfa AF: 0.557 Hom.: 49025

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

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: rs2809658; hg19: chr1-43050396;