rs4700382

Variant names:

• chr5-56586608-T-C
• rs4700382
• ENST00000648716.1:n.211+19414A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648716.1(C5orf67):​n.211+19414A>G 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 152,132 control chromosomes in the GnomAD database, including 47,284 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 0.78 (47284 hom., cov: 32)
• Consequence: C5orf67 ENST00000648716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.235+19414A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000648716.1	n.211+19414A>G		intron_variant	Intron 1 of 5
C5orf67	ENST00000810738.1	n.59-14728A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119323 AN: 152014 Hom.: 47255 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.849

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.785 AC: 119405 AN: 152132 Hom.: 47284 Cov.: 32 AF XY: 0.786 AC XY: 58468 AN XY: 74368

African (AFR) AF: 0.884 AC: 36720 AN: 41550

American (AMR) AF: 0.806 AC: 12314 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2688 AN: 3468

East Asian (EAS) AF: 0.641 AC: 3301 AN: 5150

South Asian (SAS) AF: 0.847 AC: 4079 AN: 4814

European-Finnish (FIN) AF: 0.748 AC: 7905 AN: 10574

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49971 AN: 67978

Other (OTH) AF: 0.794 AC: 1675 AN: 2110

Alfa AF: 0.752 Hom.: 85702

Bravo AF: 0.789

Asia WGS AF: 0.783 AC: 2723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	11
DANN	Benign	0.49
PhyloP100		0.53

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

Other links and lift over

dbSNP: rs4700382; hg19: chr5-55882435;