rs6449558

Positions:

• chr5-61789725-C-T

Variant summary

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

The ENST00000667197.1(C5orf64):​n.814-1049C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 151,950 control chromosomes in the GnomAD database, including 11,961 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 0.38 (11961 hom., cov: 31)
• Consequence: C5orf64 ENST00000667197.1 intron, non_coding_transcript
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C5orf64	ENST00000667197.1	n.814-1049C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57209 AN: 151830 Hom.: 11945 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.377 AC: 57260 AN: 151950 Hom.: 11961 Cov.: 31 AF XY: 0.371 AC XY: 27576 AN XY: 74288

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.377

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.342

Alfa AF: 0.318 Hom.: 16555

Bravo AF: 0.388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6449558; hg19: chr5-61085552;