ENST00000611197.2:n.98-9772G>A

Variant names:

• chr5-56565959-C-T
• rs9686661
• ENST00000611197.2:n.98-9772G>A

Variant summary

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

The ENST00000611197.2(C5orf67):​n.98-9772G>A variant causes a intron 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 ENST00000611197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 94 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=-0.89).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf67	NR_161255.1		n.236-9772G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf67	ENST00000611197.2	TSL:5	n.98-9772G>A		intron	N/A
	C5orf67	ENST00000648716.1		n.212-9772G>A		intron	N/A
	C5orf67	ENST00000810738.1		n.426+5554G>A		intron	N/A

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

African (AFR) AF: 0.231 AC: 9591 AN: 41472

American (AMR) AF: 0.224 AC: 3431 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.112 AC: 580 AN: 5174

South Asian (SAS) AF: 0.163 AC: 785 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1636 AN: 10596

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13297 AN: 67996

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.196 Hom.: 8880

Bravo AF: 0.210

Asia WGS AF: 0.176 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		-0.23

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9686661;

hg19: chr5-55861786;