5-56510924-A-G

Variant names:

• chr5-56510924-A-G
• rs459193
• ENST00000611197.2:n.1294T>C

Variant summary

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

The ENST00000611197.2(C5orf67):​n.1294T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,088 control chromosomes in the GnomAD database, including 36,065 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 0.68 (36065 hom., cov: 32)
• Consequence: C5orf67 ENST00000611197.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 141 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 (AMR) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000611197.2	n.1294T>C		non_coding_transcript_exon_variant	Exon 6 of 6	5
C5orf67	ENST00000810738.1	n.501-9462T>C		intron_variant	Intron 3 of 4
C5orf67	ENST00000810744.1	n.305+518T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103995 AN: 151968 Hom.: 36054 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.684 AC: 104045 AN: 152088 Hom.: 36065 Cov.: 32 AF XY: 0.681 AC XY: 50602 AN XY: 74338

African (AFR) AF: 0.582 AC: 24124 AN: 41462

American (AMR) AF: 0.750 AC: 11463 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2826 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2585 AN: 5168

South Asian (SAS) AF: 0.629 AC: 3025 AN: 4810

European-Finnish (FIN) AF: 0.676 AC: 7145 AN: 10564

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50523 AN: 68010

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.719 Hom.: 114803

Bravo AF: 0.685

Asia WGS AF: 0.527 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.32
DANN	Benign	0.40
PhyloP100		-0.068

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs459193; hg19: chr5-55806751;