1-42504430-G-A

Variant names:

• chr1-42504430-G-A
• rs1160467
• NM_001395517.1:c.456+5514G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001395517.1(CCDC30):​c.456+5514G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00815 in 152,210 control chromosomes in the GnomAD database, including 12 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 0.0082 (12 hom., cov: 33)
• Consequence: CCDC30 NM_001395517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 2 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=-0.93).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00815 (1241/152210) while in subpopulation AFR AF = 0.0271 (1124/41516). AF 95% confidence interval is 0.0258. There are 12 homozygotes in GnomAd4. There are 595 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 12 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395517.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC30	NM_001395517.1	MANE Select	c.456+5514G>A		intron	N/A	NP_001382446.1
	CCDC30	NM_001395379.1		c.456+5514G>A		intron	N/A	NP_001382308.1
	CCDC30	NM_001395382.1		c.456+5514G>A		intron	N/A	NP_001382311.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC30	ENST00000657597.2	MANE Select	c.456+5514G>A		intron	N/A	ENSP00000499662.2
	CCDC30	ENST00000477155.6	TSL:1	n.*433+5514G>A		intron	N/A	ENSP00000421479.3
	CCDC30	ENST00000507855.5	TSL:1	n.516+5514G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00817 AC: 1242 AN: 152092 Hom.: 12 Cov.: 33

Gnomad AFR AF: 0.0272

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00602

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000103

Gnomad OTH AF: 0.00813

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

GnomAD4 genome AF: 0.00815 AC: 1241 AN: 152210 Hom.: 12 Cov.: 33 AF XY: 0.00799 AC XY: 595 AN XY: 74432

African (AFR) AF: 0.0271 AC: 1124 AN: 41516

American (AMR) AF: 0.00602 AC: 92 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10604

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000103 AC: 7 AN: 68010

Other (OTH) AF: 0.00805 AC: 17 AN: 2112

Alfa AF: 0.00272 Hom.: 1

Bravo AF: 0.00904

Asia WGS AF: 0.00202 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.3
DANN	Benign	0.25
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs1160467; hg19: chr1-42970101;