5-61724995-G-A

Position:

• chr5-61724995-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000510414.4(C5orf64):​n.405-5051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0224 in 152,172 control chromosomes in the GnomAD database, including 84 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 0.022 (84 hom., cov: 32)
• Consequence: C5orf64 ENST00000510414.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

Genes affected

C5orf64 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0224 (3405/152172) while in subpopulation AFR AF= 0.0477 (1980/41476). AF 95% confidence interval is 0.046. There are 84 homozygotes in gnomad4. There are 1793 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 84 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf64	NR_126524.1	n.384-5051G>A		intron_variant
C5orf64	NR_126525.1	n.67-5051G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf64	ENST00000507461.2	n.140-23607G>A		intron_variant		4
C5orf64	ENST00000510414.4	n.405-5051G>A		intron_variant		3
C5orf64	ENST00000511407.1	n.67-5051G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3390 AN: 152052 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0330

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00794

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0224 AC: 3405 AN: 152172 Hom.: 84 Cov.: 32 AF XY: 0.0241 AC XY: 1793 AN XY: 74392

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.0328

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.00794

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.00995 Hom.: 11

Bravo AF: 0.0208

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.0
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514917; hg19: chr5-61020822;