chr5-115513027-A-C

Variant names:

• chr5-115513027-A-C
• rs35690726
• ENST00000502314.1:n.951A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 18 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502314.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCT5P1	ENST00000502314.1	TSL:6	n.951A>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.00417 AC: 74 AN: 17754

American (AMR) AF: 0.0115 AC: 501 AN: 43640

Ashkenazi Jewish (ASJ) AF: 0.0194 AC: 407 AN: 20970

East Asian (EAS) AF: 0.0000555 AC: 2 AN: 36042

South Asian (SAS) AF: 0.00978 AC: 683 AN: 69850

European-Finnish (FIN) AF: 0.0238 AC: 1257 AN: 52916

Middle Eastern (MID) AF: 0.0378 AC: 116 AN: 3068

European-Non Finnish (NFE) AF: 0.0238 AC: 8456 AN: 355670

Other (OTH) AF: 0.0202 AC: 669 AN: 33056

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

African (AFR) AF: 0.00358 AC: 149 AN: 41568

American (AMR) AF: 0.0112 AC: 171 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5174

South Asian (SAS) AF: 0.00600 AC: 29 AN: 4832

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10614

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0232 AC: 1577 AN: 68014

Other (OTH) AF: 0.0204 AC: 43 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		4.8

Splicing

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

Other links and lift over

dbSNP: rs35690726; hg19: chr5-114848724;