rs456867

Positions:

• chr5-56515265-C-T

Variant summary

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

The NR_161255.1(C5orf67):​n.456-1340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,150 control chromosomes in the GnomAD database, including 2,845 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 0.19 (2845 hom., cov: 33)
• Consequence: C5orf67 NR_161255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838

Genes affected

C5orf67 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.456-1340G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000611197.1	n.176-1340G>A		intron_variant		5
C5orf67	ENST00000648716.1	n.432-1340G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28928 AN: 152030 Hom.: 2837 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.190 AC: 28955 AN: 152150 Hom.: 2845 Cov.: 33 AF XY: 0.193 AC XY: 14396 AN XY: 74400

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.196

Alfa AF: 0.179 Hom.: 5333

Bravo AF: 0.184

Asia WGS AF: 0.344 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.46

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: rs456867; hg19: chr5-55811092;