rs6877842

Variant names:

• chr5-31532531-G-C
• rs6877842
• NM_018356.3:c.81+58G>C

Variant summary

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

The NM_018356.3(C5orf22):​c.81+58G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,463,870 control chromosomes in the GnomAD database, including 19,342 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 0.16 (2058 hom., cov: 30)
  • Exomes 𝑓: 0.16 (17284 hom.)
• Consequence: C5orf22 NM_018356.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 36 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C5orf22	NM_018356.3	c.81+58G>C		intron_variant	Intron 1 of 8	ENST00000325366.14	NP_060826.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf22	ENST00000325366.14	c.81+58G>C		intron_variant	Intron 1 of 8	1	NM_018356.3	ENSP00000326879.9

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24330 AN: 151718 Hom.: 2057 Cov.: 30

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.186

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.156

GnomAD4 exome AF: 0.159 AC: 208717 AN: 1312034 Hom.: 17284 AF XY: 0.159 AC XY: 103906 AN XY: 655374

African (AFR) AF: 0.188 AC: 5679 AN: 30202

American (AMR) AF: 0.132 AC: 5303 AN: 40236

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 3844 AN: 23082

East Asian (EAS) AF: 0.0181 AC: 700 AN: 38644

South Asian (SAS) AF: 0.124 AC: 9733 AN: 78530

European-Finnish (FIN) AF: 0.129 AC: 6677 AN: 51946

Middle Eastern (MID) AF: 0.166 AC: 885 AN: 5330

European-Non Finnish (NFE) AF: 0.169 AC: 167243 AN: 988976

Other (OTH) AF: 0.157 AC: 8653 AN: 55088

GnomAD4 genome AF: 0.160 AC: 24336 AN: 151836 Hom.: 2058 Cov.: 30 AF XY: 0.158 AC XY: 11701 AN XY: 74178

African (AFR) AF: 0.184 AC: 7634 AN: 41418

American (AMR) AF: 0.156 AC: 2382 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3472

East Asian (EAS) AF: 0.0233 AC: 119 AN: 5106

South Asian (SAS) AF: 0.124 AC: 596 AN: 4812

European-Finnish (FIN) AF: 0.124 AC: 1300 AN: 10510

Middle Eastern (MID) AF: 0.190 AC: 55 AN: 290

European-Non Finnish (NFE) AF: 0.165 AC: 11245 AN: 67950

Other (OTH) AF: 0.155 AC: 327 AN: 2104

Alfa AF: 0.156 Hom.: 251

Bravo AF: 0.166

Asia WGS AF: 0.0920 AC: 318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.51
PhyloP100		1.6
PromoterAI		-0.017	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs6877842; hg19: chr5-31532638; COSMIC: COSV57598375; COSMIC: COSV57598375;