chr5-56564125-A-G

Position:

• chr5-56564125-A-G

Variant summary

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

The NR_161255.1(C5orf67):​n.236-7938T>C 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 0.209 in 152,222 control chromosomes in the GnomAD database, including 3,387 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 0.21 (3387 hom., cov: 32)
• Consequence: C5orf67 NR_161255.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C5orf67	NR_161255.1	n.236-7938T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf67	ENST00000648716.1	n.212-7938T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31727 AN: 152104 Hom.: 3387 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.209 AC: 31747 AN: 152222 Hom.: 3387 Cov.: 32 AF XY: 0.206 AC XY: 15312 AN XY: 74428

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.220

Alfa AF: 0.198 Hom.: 406

Bravo AF: 0.216

Asia WGS AF: 0.179 AC: 621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.65
DANN	Benign	0.45

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: rs11743303; hg19: chr5-55859952; COSMIC: COSV71246381;