5-61729255-A-T

Position:

• chr5-61729255-A-T

Variant summary

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

The ENST00000667197.1(C5orf64):​n.399-19347A>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 0.213 in 152,086 control chromosomes in the GnomAD database, including 3,761 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 0.21 (3761 hom., cov: 32)
• Consequence: C5orf64 ENST00000667197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf64	NR_126524.1	n.384-791A>T		intron_variant, non_coding_transcript_variant
C5orf64	NR_126525.1	n.67-791A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf64	ENST00000667197.1	n.399-19347A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32387 AN: 151968 Hom.: 3759 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.213 AC: 32404 AN: 152086 Hom.: 3761 Cov.: 32 AF XY: 0.212 AC XY: 15752 AN XY: 74354

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.216

Alfa AF: 0.206 Hom.: 420

Bravo AF: 0.212

Asia WGS AF: 0.185 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4699982; hg19: chr5-61025082;