5-56507706-G-A

Variant names:

• chr5-56507706-G-A
• rs30000
• ENST00000810738.1:n.501-6244C>T

Variant summary

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

The ENST00000810738.1(C5orf67):​n.501-6244C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,020 control chromosomes in the GnomAD database, including 28,330 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 0.57 (28330 hom., cov: 32)
• Consequence: C5orf67 ENST00000810738.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 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	ENST00000810738.1	n.501-6244C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86282 AN: 151900 Hom.: 28329 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.568 AC: 86288 AN: 152020 Hom.: 28330 Cov.: 32 AF XY: 0.565 AC XY: 41943 AN XY: 74300

African (AFR) AF: 0.242 AC: 10024 AN: 41444

American (AMR) AF: 0.651 AC: 9947 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2820 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5180

South Asian (SAS) AF: 0.611 AC: 2938 AN: 4810

European-Finnish (FIN) AF: 0.665 AC: 7002 AN: 10530

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.739 AC: 50247 AN: 67998

Other (OTH) AF: 0.599 AC: 1263 AN: 2108

Alfa AF: 0.644 Hom.: 4226

Bravo AF: 0.552

Asia WGS AF: 0.414 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs30000; hg19: chr5-55803533;