11-83273852-G-T

Variant names:

• chr11-83273852-G-T
• rs1030353364
• NM_021825.5:c.481C>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_021825.5(CCDC90B):​c.481C>A​(p.Arg161Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,455,972 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: CCDC90B NM_021825.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.25
• Publications: 0 publications found

Genes affected

CCDC90B (HGNC:28108): (coiled-coil domain containing 90B) Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BP7: Synonymous conserved (PhyloP=3.25 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021825.5. 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
	CCDC90B	NM_021825.5	MANE Select	c.481C>A	p.Arg161Arg	synonymous	Exon 6 of 9	NP_068597.2
	CCDC90B	NM_001286118.3		c.187C>A	p.Arg63Arg	synonymous	Exon 5 of 8	NP_001273047.1
	CCDC90B	NM_001286119.3		c.187C>A	p.Arg63Arg	synonymous	Exon 6 of 9	NP_001273048.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC90B	ENST00000529689.6	TSL:1 MANE Select	c.481C>A	p.Arg161Arg	synonymous	Exon 6 of 9	ENSP00000434724.1	Q9GZT6-1
	CCDC90B	ENST00000455220.6	TSL:1	c.178C>A	p.Arg60Arg	synonymous	Exon 6 of 9	ENSP00000390990.3	Q9GZT6-3
	CCDC90B	ENST00000525503.5	TSL:1	n.*669C>A		non_coding_transcript_exon	Exon 6 of 9	ENSP00000431424.2	E9PSG6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1455972 Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2 AN XY: 724006

African (AFR) AF: 0.00 AC: 0 AN: 33264

American (AMR) AF: 0.00 AC: 0 AN: 44112

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25928

East Asian (EAS) AF: 0.0000507 AC: 2 AN: 39472

South Asian (SAS) AF: 0.00 AC: 0 AN: 85262

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53098

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5744

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1108964

Other (OTH) AF: 0.00 AC: 0 AN: 60128

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	7.9
DANN	Benign	0.66
PhyloP100		3.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs1030353364; hg19: chr11-82984895;