rs895381

Variant names:

• chr5-61611974-T-C
• rs895381
• ENST00000654772.1:n.207+1259T>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf64	ENST00000654772.1	n.207+1259T>C		intron_variant	Intron 1 of 3
C5orf64	ENST00000657803.1	n.171+1259T>C		intron_variant	Intron 1 of 3
C5orf64	ENST00000659478.1	n.207+1259T>C		intron_variant	Intron 1 of 4

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;