5-61611974-T-C

Position:

• chr5-61611974-T-C

Variant summary

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

The ENST00000654772.1(C5orf64):​n.207+1259T>C 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 0.552 in 152,086 control chromosomes in the GnomAD database, including 24,094 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 0.55 (24094 hom., cov: 32)
• Consequence: C5orf64 ENST00000654772.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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	ENST00000654772.1	n.207+1259T>C		intron_variant, non_coding_transcript_variant
C5orf64	ENST00000657803.1	n.171+1259T>C		intron_variant, non_coding_transcript_variant
C5orf64	ENST00000659478.1	n.207+1259T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83862 AN: 151968 Hom.: 24075 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.552 AC: 83917 AN: 152086 Hom.: 24094 Cov.: 32 AF XY: 0.562 AC XY: 41753 AN XY: 74342

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.583

Alfa AF: 0.578 Hom.: 11902

Bravo AF: 0.544

Asia WGS AF: 0.734 AC: 2553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.94
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs895381; hg19: chr5-60907801;