chr3-48445934-A-G

Variant names:

• chr3-48445934-A-G
• rs9876781
• XM_011534113.3:c.-14+325T>C

Variant summary

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

The ENST00000438872.1(ENSG00000244380):​n.374+325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 151,918 control chromosomes in the GnomAD database, including 24,533 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 0.57 (24533 hom., cov: 32)
• Consequence: ENSG00000244380 ENST00000438872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 34 publications found

Genes affected

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]

ENSG00000244380 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=4.777).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438872.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000244380	ENST00000435578.1	TSL:4	n.323+400T>C		intron	N/A
	ENSG00000244380	ENST00000438872.1	TSL:3	n.374+325T>C		intron	N/A
	ENSG00000244380	ENST00000793352.1		n.347+400T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86128 AN: 151798 Hom.: 24511 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.567 AC: 86195 AN: 151918 Hom.: 24533 Cov.: 32 AF XY: 0.574 AC XY: 42628 AN XY: 74254

African (AFR) AF: 0.540 AC: 22390 AN: 41426

American (AMR) AF: 0.662 AC: 10107 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1786 AN: 3464

East Asian (EAS) AF: 0.697 AC: 3604 AN: 5168

South Asian (SAS) AF: 0.676 AC: 3258 AN: 4818

European-Finnish (FIN) AF: 0.607 AC: 6387 AN: 10528

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36780 AN: 67924

Other (OTH) AF: 0.576 AC: 1217 AN: 2112

Alfa AF: 0.550 Hom.: 46909

Bravo AF: 0.569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	4.8
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9876781;