rs4129540

Positions:

• chr5-56583031-C-G
• chr5-56583031-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161255.1(C5orf67):​n.235+22991G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,204 control chromosomes in the GnomAD database, including 46,638 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 (46638 hom., cov: 33)
• Consequence: C5orf67 NR_161255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

C5orf67 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.235+22991G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000648716.1	n.211+22991G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118382 AN: 152086 Hom.: 46602 Cov.: 33

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.778 AC: 118471 AN: 152204 Hom.: 46638 Cov.: 33 AF XY: 0.779 AC XY: 57990 AN XY: 74408

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.850

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.791

Alfa AF: 0.739 Hom.: 4933

Bravo AF: 0.783

Asia WGS AF: 0.800 AC: 2782 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129540; hg19: chr5-55878858;