1-42586800-T-G

Variant names:

• chr1-42586800-T-G
• rs12408987
• NM_001395517.1:c.1686-2521T>G

Variant summary

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

The NM_001395517.1(CCDC30):​c.1686-2521T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,172 control chromosomes in the GnomAD database, including 1,430 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 0.13 (1430 hom., cov: 31)
• Consequence: CCDC30 NM_001395517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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 = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC30	NM_001395517.1	c.1686-2521T>G		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.1686-2521T>G		intron_variant	Intron 13 of 20		NM_001395517.1	ENSP00000499662.2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19298 AN: 152054 Hom.: 1431 Cov.: 31

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.127 AC: 19295 AN: 152172 Hom.: 1430 Cov.: 31 AF XY: 0.124 AC XY: 9253 AN XY: 74392

Gnomad4 AFR AF: 0.0611

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.149

Alfa AF: 0.150 Hom.: 498

Bravo AF: 0.132

Asia WGS AF: 0.132 AC: 456 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	1.0
DANN	Benign	0.59

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: rs12408987; hg19: chr1-43052471;