rs4867349

Variant names:

• chr5-31536220-G-A
• rs4867349
• NM_018356.3:c.377+327G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-31536220-G-A
• chr5-31536220-G-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.377+327G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 152,122 control chromosomes in the GnomAD database, including 47,142 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 0.79 (47142 hom., cov: 32)
• Consequence: C5orf22 NM_018356.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018356.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf22	NM_018356.3	MANE Select	c.377+327G>A		intron	N/A	NP_060826.2
	C5orf22	NR_134298.2		n.469+327G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf22	ENST00000325366.14	TSL:1 MANE Select	c.377+327G>A		intron	N/A	ENSP00000326879.9
	C5orf22	ENST00000510659.5	TSL:1	n.377+327G>A		intron	N/A	ENSP00000423039.1
	C5orf22	ENST00000926221.1		c.135+1895G>A		intron	N/A	ENSP00000596280.1

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119327 AN: 152004 Hom.: 47094 Cov.: 32

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.785 AC: 119432 AN: 152122 Hom.: 47142 Cov.: 32 AF XY: 0.783 AC XY: 58231 AN XY: 74360

African (AFR) AF: 0.850 AC: 35281 AN: 41488

American (AMR) AF: 0.756 AC: 11550 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2449 AN: 3472

East Asian (EAS) AF: 0.623 AC: 3222 AN: 5174

South Asian (SAS) AF: 0.742 AC: 3581 AN: 4824

European-Finnish (FIN) AF: 0.749 AC: 7910 AN: 10558

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.778 AC: 52903 AN: 68014

Other (OTH) AF: 0.789 AC: 1666 AN: 2112

Alfa AF: 0.777 Hom.: 68351

Bravo AF: 0.790

Asia WGS AF: 0.675 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.032
DANN	Benign	0.50
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs4867349; hg19: chr5-31536327;