rs17410035

chr5-31541035-G-T

Variant summary

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

The NM_018356.3(C5orf22):c.870+24G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,557,702 control chromosomes in the GnomAD database, including 76,909 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 0.24 (5351 hom., cov: 31)
  • Exomes 𝑓: 0.31 (71558 hom.)
• Consequence: C5orf22 NM_018356.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942

Genes affected

C5orf22 (HGNC:25639): (chromosome 5 open reading frame 22)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C5orf22	NM_018356.3	c.870+24G>T		intron_variant		ENST00000325366.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf22	ENST00000325366.14	c.870+24G>T		intron_variant		1	NM_018356.3	P1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 36915 AN: 150732 Hom.: 5346 Cov.: 31

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.248

GnomAD3 exomes AF: 0.276 AC: 67041 AN: 243230 Hom.: 10078 AF XY: 0.286 AC XY: 37719 AN XY: 131732

Gnomad AFR exome AF: 0.0896

Gnomad AMR exome AF: 0.189

Gnomad ASJ exome AF: 0.317

Gnomad EAS exome AF: 0.167

Gnomad SAS exome AF: 0.326

Gnomad FIN exome AF: 0.260

Gnomad NFE exome AF: 0.330

Gnomad OTH exome AF: 0.288

GnomAD4 exome AF: 0.311 AC: 437865 AN: 1406858 Hom.: 71558 Cov.: 25 AF XY: 0.313 AC XY: 220004 AN XY: 702700

Gnomad4 AFR exome AF: 0.0820

Gnomad4 AMR exome AF: 0.190

Gnomad4 ASJ exome AF: 0.313

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.325

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.332

Gnomad4 OTH exome AF: 0.293

GnomAD4 genome AF: 0.245 AC: 36931 AN: 150844 Hom.: 5351 Cov.: 31 AF XY: 0.242 AC XY: 17799 AN XY: 73628

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.249

Alfa AF: 0.313 Hom.: 13425

Bravo AF: 0.230

Asia WGS AF: 0.212 AC: 743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.4
Dann	Benign	0.73

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: rs17410035; hg19: chr5-31541142; COSMIC: COSV57598573; COSMIC: COSV57598573;