5-115513027-A-C

Position:

• chr5-115513027-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000502314.1(CCT5P1):​n.951A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0184 in 785,254 control chromosomes in the GnomAD database, including 178 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 0.015 (18 hom., cov: 32)
  • Exomes 𝑓: 0.019 (160 hom.)
• Consequence: CCT5P1 ENST00000502314.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.84

Genes affected

CCT5P1 (HGNC:35135): (chaperonin containing TCP1 subunit 5 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0151 (2305/152288) while in subpopulation NFE AF= 0.0232 (1577/68014). AF 95% confidence interval is 0.0222. There are 18 homozygotes in gnomad4. There are 1112 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCT5P1	ENST00000502314.1	n.951A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0151 AC: 2305 AN: 152170 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.00360

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0112

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0206

GnomAD4 exome AF: 0.0192 AC: 12165 AN: 632966 Hom.: 160 Cov.: 6 AF XY: 0.0188 AC XY: 6494 AN XY: 344520

Gnomad4 AFR exome AF: 0.00417

Gnomad4 AMR exome AF: 0.0115

Gnomad4 ASJ exome AF: 0.0194

Gnomad4 EAS exome AF: 0.0000555

Gnomad4 SAS exome AF: 0.00978

Gnomad4 FIN exome AF: 0.0238

Gnomad4 NFE exome AF: 0.0238

Gnomad4 OTH exome AF: 0.0202

GnomAD4 genome AF: 0.0151 AC: 2305 AN: 152288 Hom.: 18 Cov.: 32 AF XY: 0.0149 AC XY: 1112 AN XY: 74460

Gnomad4 AFR AF: 0.00358

Gnomad4 AMR AF: 0.0112

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00600

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0232

Gnomad4 OTH AF: 0.0204

Alfa AF: 0.0194 Hom.: 2

Bravo AF: 0.0137

Asia WGS AF: 0.00346 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	1.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35690726; hg19: chr5-114848724;