rs10519919

Positions:

• chr5-127065120-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001164478.2(C5orf63):​c.-7-6118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,306 control chromosomes in the GnomAD database, including 77 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 0.020 (77 hom., cov: 32)
• Consequence: C5orf63 NM_001164478.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.792

Genes affected

C5orf63 (HGNC:40051): (chromosome 5 open reading frame 63)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C5orf63	NM_001164478.2	c.-7-6118A>G		intron_variant		ENST00000296662.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf63	ENST00000296662.10	c.-7-6118A>G		intron_variant		5	NM_001164478.2	P1

Frequencies

GnomAD3 genomes AF: 0.0205 AC: 3122 AN: 152188 Hom.: 77 Cov.: 32

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0297

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0205 AC: 3116 AN: 152306 Hom.: 77 Cov.: 32 AF XY: 0.0232 AC XY: 1729 AN XY: 74484

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0127

Gnomad4 ASJ AF: 0.0403

Gnomad4 EAS AF: 0.0912

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0297

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0165

Alfa AF: 0.0131 Hom.: 5

Bravo AF: 0.0170

Asia WGS AF: 0.0710 AC: 245 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	6.2
DANN	Benign	0.76

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519919; hg19: chr5-126400812;