ENST00000611197.2:n.318-1340G>A

Variant names:

• chr5-56515265-C-T
• rs456867
• ENST00000611197.2:n.318-1340G>A

Variant summary

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

The ENST00000611197.2(C5orf67):​n.318-1340G>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 ENST00000611197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• Publications: 9 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=-0.84).
• 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 rank	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.456-1340G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000611197.2	n.318-1340G>A		intron_variant	Intron 4 of 5	5
C5orf67	ENST00000648716.1	n.432-1340G>A		intron_variant	Intron 4 of 5
C5orf67	ENST00000810738.1	n.501-13803G>A		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.194 AC: 8059 AN: 41506

American (AMR) AF: 0.161 AC: 2460 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1740 AN: 5170

South Asian (SAS) AF: 0.285 AC: 1374 AN: 4826

European-Finnish (FIN) AF: 0.229 AC: 2424 AN: 10578

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11861 AN: 67990

Other (OTH) AF: 0.196 AC: 413 AN: 2110

Alfa AF: 0.181 Hom.: 8199

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
PhyloP100		0.84

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: rs456867; hg19: chr5-55811092;