rs13178221

Positions:

• chr5-56601624-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.235+4398G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,124 control chromosomes in the GnomAD database, including 2,853 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 0.18 (2853 hom., cov: 32)
• Consequence: C5orf67 NR_161255.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

C5orf67 (HGNC:51252): (chromosome 5 putative open reading frame 67)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.235+4398G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000648716.1	n.211+4398G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27298 AN: 152004 Hom.: 2854 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27298 AN: 152124 Hom.: 2853 Cov.: 32 AF XY: 0.177 AC XY: 13196 AN XY: 74358

Gnomad4 AFR AF: 0.0972

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.190

Alfa AF: 0.226 Hom.: 6059

Bravo AF: 0.171

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.78

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: rs13178221; hg19: chr5-55897451;