5-56582853-A-G

Variant names:

• chr5-56582853-A-G
• rs4129542
• ENST00000611197.2:n.97+2772T>C

Variant summary

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

The ENST00000611197.2(C5orf67):​n.97+2772T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,218 control chromosomes in the GnomAD database, including 984 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 0.10 (984 hom., cov: 32)
• Consequence: C5orf67 ENST00000611197.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C5orf67	NR_161255.1	n.235+23169T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf67	ENST00000611197.2	n.97+2772T>C		intron_variant	Intron 1 of 5	5
C5orf67	ENST00000648716.1	n.211+23169T>C		intron_variant	Intron 1 of 5
C5orf67	ENST00000810738.1	n.59-10973T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15920 AN: 152100 Hom.: 983 Cov.: 32

Gnomad AFR AF: 0.0508

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.105 AC: 15916 AN: 152218 Hom.: 984 Cov.: 32 AF XY: 0.103 AC XY: 7640 AN XY: 74426

African (AFR) AF: 0.0507 AC: 2108 AN: 41558

American (AMR) AF: 0.0848 AC: 1297 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 579 AN: 3470

East Asian (EAS) AF: 0.0374 AC: 194 AN: 5182

South Asian (SAS) AF: 0.0714 AC: 345 AN: 4832

European-Finnish (FIN) AF: 0.119 AC: 1258 AN: 10592

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9799 AN: 67980

Other (OTH) AF: 0.118 AC: 249 AN: 2108

Alfa AF: 0.116 Hom.: 910

Bravo AF: 0.0996

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.1
DANN	Benign	0.80
PhyloP100		0.25

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: rs4129542; hg19: chr5-55878680; COSMIC: COSV71246429;