5-56582931-T-A

Variant names:

• chr5-56582931-T-A
• rs4129541
• ENST00000611197.2:n.97+2694A>T

Variant summary

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

The ENST00000611197.2(C5orf67):​n.97+2694A>T 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 152,182 control chromosomes in the GnomAD database, including 46,623 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 (46623 hom., cov: 32)
• Consequence: C5orf67 ENST00000611197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 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.235+23091A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C5orf67	ENST00000611197.2	TSL:5	n.97+2694A>T		intron	N/A
	C5orf67	ENST00000648716.1		n.211+23091A>T		intron	N/A
	C5orf67	ENST00000810738.1		n.59-11051A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118354 AN: 152064 Hom.: 46587 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.715

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: 118443 AN: 152182 Hom.: 46623 Cov.: 32 AF XY: 0.779 AC XY: 57966 AN XY: 74384

African (AFR) AF: 0.895 AC: 37164 AN: 41528

American (AMR) AF: 0.793 AC: 12123 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2644 AN: 3464

East Asian (EAS) AF: 0.672 AC: 3476 AN: 5176

South Asian (SAS) AF: 0.850 AC: 4103 AN: 4826

European-Finnish (FIN) AF: 0.744 AC: 7866 AN: 10568

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48658 AN: 68010

Other (OTH) AF: 0.792 AC: 1672 AN: 2112

Alfa AF: 0.745 Hom.: 5327

Bravo AF: 0.784

Asia WGS AF: 0.800 AC: 2779 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		-0.044

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: rs4129541; hg19: chr5-55878758;