22-29058489-T-C

Variant names:

• chr22-29058489-T-C
• rs6005975
• NM_015370.2:c.*253A>G

Variant summary

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

The NM_015370.2(C22orf31):​c.*253A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,944 control chromosomes in the GnomAD database, including 26,394 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 0.58 (26394 hom., cov: 30)
• Consequence: C22orf31 NM_015370.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 10 publications found

Genes affected

C22orf31 (HGNC:26931): (chromosome 22 open reading frame 31)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015370.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C22orf31	NM_015370.2	MANE Select	c.*253A>G		downstream_gene	N/A	NP_056185.1
	C22orf31	NM_001386866.1		c.*253A>G		downstream_gene	N/A	NP_001373795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C22orf31	ENST00000216071.5	TSL:1 MANE Select	c.*253A>G		downstream_gene	N/A	ENSP00000216071.4

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88241 AN: 151826 Hom.: 26335 Cov.: 30

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.582 AC: 88356 AN: 151944 Hom.: 26394 Cov.: 30 AF XY: 0.582 AC XY: 43246 AN XY: 74268

African (AFR) AF: 0.715 AC: 29634 AN: 41460

American (AMR) AF: 0.547 AC: 8354 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1994 AN: 3472

East Asian (EAS) AF: 0.616 AC: 3165 AN: 5140

South Asian (SAS) AF: 0.636 AC: 3069 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5674 AN: 10548

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34758 AN: 67934

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.526 Hom.: 44113

Bravo AF: 0.584

Asia WGS AF: 0.643 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs6005975; hg19: chr22-29454477;