rs4867349

Positions:

• chr5-31536220-G-A
• chr5-31536220-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C5orf22	NM_018356.3	c.377+327G>A		intron_variant		ENST00000325366.14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf22	ENST00000325366.14	c.377+327G>A		intron_variant		1	NM_018356.3	P1

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

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.789

Alfa AF: 0.775 Hom.: 57127

Bravo AF: 0.790

Asia WGS AF: 0.675 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.032
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs4867349; hg19: chr5-31536327;