chr5-56604369-C-T

Variant names:

• chr5-56604369-C-T
• rs9292118
• ENST00000648716.1:n.211+1653G>A

Variant summary

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

The ENST00000648716.1(C5orf67):​n.211+1653G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,002 control chromosomes in the GnomAD database, including 11,575 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 0.34 (11575 hom., cov: 32)
• Consequence: C5orf67 ENST00000648716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.235+1653G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000648716.1	n.211+1653G>A		intron_variant	Intron 1 of 5
C5orf67	ENST00000810738.1	n.59-32489G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52020 AN: 151886 Hom.: 11563 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.343 AC: 52067 AN: 152002 Hom.: 11575 Cov.: 32 AF XY: 0.334 AC XY: 24828 AN XY: 74296

African (AFR) AF: 0.633 AC: 26193 AN: 41408

American (AMR) AF: 0.217 AC: 3315 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3472

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5182

South Asian (SAS) AF: 0.265 AC: 1279 AN: 4826

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10558

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17249 AN: 67976

Other (OTH) AF: 0.301 AC: 632 AN: 2100

Alfa AF: 0.275 Hom.: 5232

Bravo AF: 0.354

Asia WGS AF: 0.172 AC: 598 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	1.7
DANN	Benign	0.93
PhyloP100		-0.27

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: rs9292118; hg19: chr5-55900196;