rs10514920

Variant names:

• chr5-61768636-T-A
• rs10514920
• ENST00000667197.1:n.813+12692T>A

Variant summary

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

The ENST00000667197.1(C5orf64):​n.813+12692T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 152,302 control chromosomes in the GnomAD database, including 44 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 0.021 (44 hom., cov: 32)
• Consequence: C5orf64 ENST00000667197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

C5orf64 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0207 (3157/152302) while in subpopulation AFR AF= 0.0346 (1438/41558). AF 95% confidence interval is 0.0331. There are 44 homozygotes in gnomad4. There are 1664 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 44 gene

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
C5orf64	ENST00000667197.1	n.813+12692T>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.0207 AC: 3147 AN: 152184 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00981

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.00924

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0499

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0113

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0207 AC: 3157 AN: 152302 Hom.: 44 Cov.: 32 AF XY: 0.0223 AC XY: 1664 AN XY: 74484

Gnomad4 AFR AF: 0.0346

Gnomad4 AMR AF: 0.00980

Gnomad4 ASJ AF: 0.00606

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0499

Gnomad4 NFE AF: 0.0113

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0150 Hom.: 0

Bravo AF: 0.0178

Asia WGS AF: 0.0220 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514920; hg19: chr5-61064463;