5-61654384-T-G

Position:

• chr5-61654384-T-G

Variant summary

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

The ENST00000505642.6(C5orf64):​n.148+10984T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,858 control chromosomes in the GnomAD database, including 3,867 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 0.22 (3867 hom., cov: 31)
• Consequence: C5orf64 ENST00000505642.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744

Genes affected

C5orf64 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C5orf64	NR_126523.1	n.140+10984T>G		intron_variant
C5orf64	NR_126524.1	n.140+10984T>G		intron_variant
C5orf64	NR_126525.1	n.66+16538T>G		intron_variant
C5orf64	NR_161251.1	n.161+10984T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C5orf64	ENST00000505642.6	n.148+10984T>G		intron_variant		2
C5orf64	ENST00000507461.2	n.139+16538T>G		intron_variant		4
C5orf64	ENST00000510414.4	n.161+10984T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32941 AN: 151762 Hom.: 3862 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.217 AC: 32986 AN: 151858 Hom.: 3867 Cov.: 31 AF XY: 0.217 AC XY: 16138 AN XY: 74198

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.204

Alfa AF: 0.172 Hom.: 4634

Bravo AF: 0.214

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11738335; hg19: chr5-60950211;