chr22-32158153-G-C

Position:

• chr22-32158153-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010859.3(C22orf42):​c.232+831C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 151,832 control chromosomes in the GnomAD database, including 546 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 0.086 (546 hom., cov: 32)
• Consequence: C22orf42 NM_001010859.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

C22orf42 (HGNC:27160): (chromosome 22 open reading frame 42)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C22orf42	NM_001010859.3	c.232+831C>G		intron_variant		ENST00000382097.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C22orf42	ENST00000382097.4	c.232+831C>G		intron_variant		1	NM_001010859.3	P1
C22orf42	ENST00000467813.1	n.339+831C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13057 AN: 151714 Hom.: 543 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0715

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0863 AC: 13097 AN: 151832 Hom.: 546 Cov.: 32 AF XY: 0.0836 AC XY: 6209 AN XY: 74256

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0518

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.00250

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.0715

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0836 Hom.: 52

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs2981852; hg19: chr22-32554140;