5-56558326-C-T

Variant names:

• chr5-56558326-C-T
• rs6867983
• ENST00000611197.2:n.98-2139G>A

Variant summary

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

The ENST00000611197.2(C5orf67):​n.98-2139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 151,964 control chromosomes in the GnomAD database, including 2,185 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 0.16 (2185 hom., cov: 32)
• Consequence: C5orf67 ENST00000611197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 21 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611197.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf67	NR_161255.1		n.236-2139G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf67	ENST00000611197.2	TSL:5	n.98-2139G>A		intron	N/A
	C5orf67	ENST00000648716.1		n.212-2139G>A		intron	N/A
	C5orf67	ENST00000810738.1		n.426+13187G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24881 AN: 151846 Hom.: 2181 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0614

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.164 AC: 24904 AN: 151964 Hom.: 2185 Cov.: 32 AF XY: 0.163 AC XY: 12072 AN XY: 74266

African (AFR) AF: 0.231 AC: 9556 AN: 41406

American (AMR) AF: 0.185 AC: 2826 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 373 AN: 3466

East Asian (EAS) AF: 0.0617 AC: 319 AN: 5166

South Asian (SAS) AF: 0.125 AC: 601 AN: 4816

European-Finnish (FIN) AF: 0.149 AC: 1572 AN: 10560

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9172 AN: 67960

Other (OTH) AF: 0.165 AC: 348 AN: 2112

Alfa AF: 0.146 Hom.: 5103

Bravo AF: 0.171

Asia WGS AF: 0.119 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.9
DANN	Benign	0.71
PhyloP100		-0.25

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: rs6867983; hg19: chr5-55854153;