22-41695023-AAG-AAGAG

Position:

• chr22-41695023-AAG-AAGAG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000472110.3(C22orf46P):​n.1993_1994dupGA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.72 (40081 hom., cov: 0)
  • Exomes 𝑓: 0.77 (4394 hom.)
• Consequence: C22orf46P ENST00000472110.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.892

Genes affected

C22orf46P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C22orf46P	NR_160905.1	n.1907_1908dupGA		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C22orf46P	ENST00000472110.3	n.1993_1994dupGA		non_coding_transcript_exon_variant	3/3	3
C22orf46P	ENST00000654032.1	n.1781_1782dupGA		non_coding_transcript_exon_variant	2/2
C22orf46P	ENST00000656592.1	n.1905_1906dupGA		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108538 AN: 151558 Hom.: 40057 Cov.: 0

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.711

GnomAD4 exome AF: 0.766 AC: 11469 AN: 14966 Hom.: 4394 Cov.: 0 AF XY: 0.769 AC XY: 5453 AN XY: 7090

Gnomad4 AFR exome AF: 0.625

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.766

Gnomad4 NFE exome AF: 0.769

Gnomad4 OTH exome AF: 0.807

GnomAD4 genome AF: 0.716 AC: 108594 AN: 151678 Hom.: 40081 Cov.: 0 AF XY: 0.711 AC XY: 52624 AN XY: 74066

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.917

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.714

Alfa AF: 0.753 Hom.: 5359

Bravo AF: 0.688

Asia WGS AF: 0.809 AC: 2814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35117663; hg19: chr22-42091027;