8-144528767-C-T

Variant names:

• chr8-144528767-C-T
• rs777942397
• NM_001001795.2:c.150G>A

Variant summary

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

The NM_001001795.2(C8orf82):​c.150G>A​(p.Gln50Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000325 in 1,263,342 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: 31)
  • Exomes 𝑓: 0.000032 (0 hom.)
• Consequence: C8orf82 NM_001001795.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

Genes affected

C8orf82 (HGNC:33826): (chromosome 8 open reading frame 82)

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 (REVEL=0.095).
• BP7: Synonymous conserved (PhyloP=0.078 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001795.2. 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
	C8orf82	NM_001001795.2	MANE Select	c.150G>A	p.Gln50Gln	synonymous	Exon 1 of 3	NP_001001795.1	Q6P1X6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C8orf82	ENST00000524821.6	TSL:1 MANE Select	c.150G>A	p.Gln50Gln	synonymous	Exon 1 of 3	ENSP00000436621.1	Q6P1X6-1
	C8orf82	ENST00000313465.5	TSL:1	c.150G>A	p.Gln50Gln	synonymous	Exon 1 of 2	ENSP00000316262.5	J3KNI2
	C8orf82	ENST00000527462.1	TSL:3	c.295G>A	p.Gly99Arg	missense	Exon 1 of 2	ENSP00000436060.1	H0YEK9

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.0000325 AC: 41 AN: 1263342 Hom.: 0 Cov.: 35 AF XY: 0.0000407 AC XY: 25 AN XY: 613832

African (AFR) AF: 0.00 AC: 0 AN: 24782

American (AMR) AF: 0.00 AC: 0 AN: 20180

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18114

East Asian (EAS) AF: 0.00 AC: 0 AN: 29340

South Asian (SAS) AF: 0.0000346 AC: 2 AN: 57838

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45100

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3976

European-Non Finnish (NFE) AF: 0.0000375 AC: 38 AN: 1012762

Other (OTH) AF: 0.0000195 AC: 1 AN: 51250

GnomAD4 genome Cov.: 31

Alfa AF: 0.0000335 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	13
DANN	Benign	0.97
PhyloP100		0.078
PromoterAI		0.043	Neutral

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

Other links and lift over

dbSNP: rs777942397; hg19: chr8-145754151;