rs9686661

chr5-56565959-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.236-9772G>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 0.202 in 152,156 control chromosomes in the GnomAD database, including 3,202 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 0.20 (3202 hom., cov: 32)
• Consequence: C5orf67 NR_161255.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C5orf67	NR_161255.1	n.236-9772G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf67	ENST00000648716.1	n.212-9772G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30739 AN: 152038 Hom.: 3204 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.202 AC: 30745 AN: 152156 Hom.: 3202 Cov.: 32 AF XY: 0.198 AC XY: 14757 AN XY: 74376

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.217

Alfa AF: 0.194 Hom.: 3276

Bravo AF: 0.210

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.0
Dann	Benign	0.52

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: rs9686661; hg19: chr5-55861786;