rs730566

Variant names:

• chr3-48445644-C-A
• rs730566
• ENST00000435578.1:n.324-479G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-48445644-C-A
• chr3-48445644-C-G
• chr3-48445644-C-T

Variant summary

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

The ENST00000435578.1(ENSG00000244380):​n.324-479G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,210 control chromosomes in the GnomAD database, including 5,696 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 0.25 (5696 hom., cov: 33)
• Consequence: ENSG00000244380 ENST00000435578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06
• Publications: 43 publications found

Genes affected

ENSG00000244380 (HGNC:):

CCDC51 (HGNC:25714): (coiled-coil domain containing 51) Enables mitochondrial ATP-gated potassium channel activity. Involved in potassium ion transmembrane transport. Is integral component of mitochondrial inner membrane. Part of mitochondrial ATP-gated potassium channel complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC51	XM_011534113.3	c.-14+615G>T		intron_variant	Intron 1 of 4		XP_011532415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000244380	ENST00000435578.1	n.324-479G>T		intron_variant	Intron 1 of 2	4
ENSG00000244380	ENST00000438872.1	n.374+615G>T		intron_variant	Intron 1 of 1	3
ENSG00000244380	ENST00000793352.1	n.348-479G>T		intron_variant	Intron 1 of 1
ENSG00000244380	ENST00000793353.1	n.395-479G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37982 AN: 152092 Hom.: 5686 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.250 AC: 38009 AN: 152210 Hom.: 5696 Cov.: 33 AF XY: 0.255 AC XY: 18986 AN XY: 74412

African (AFR) AF: 0.110 AC: 4573 AN: 41554

American (AMR) AF: 0.382 AC: 5846 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3472

East Asian (EAS) AF: 0.634 AC: 3283 AN: 5176

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2692 AN: 10584

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18485 AN: 68002

Other (OTH) AF: 0.277 AC: 584 AN: 2112

Alfa AF: 0.267 Hom.: 24762

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.67
PhyloP100		2.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs730566; hg19: chr3-48487048;