chr5-92890507-A-G

Position:

• chr5-92890507-A-G

Variant summary

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

The ENST00000479109.2(CCT7P2):​n.334T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.408 in 597,550 control chromosomes in the GnomAD database, including 50,551 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 0.40 (12494 hom., cov: 32)
  • Exomes 𝑓: 0.41 (38057 hom.)
• Consequence: CCT7P2 ENST00000479109.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.07

Genes affected

CCT7P2 (HGNC:35134): (chaperonin containing TCP1 subunit 7 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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
CCT7P2	ENST00000479109.2	n.334T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61283 AN: 151958 Hom.: 12485 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.409 AC: 182260 AN: 445474 Hom.: 38057 Cov.: 2 AF XY: 0.410 AC XY: 99080 AN XY: 241498

Gnomad4 AFR exome AF: 0.459

Gnomad4 AMR exome AF: 0.350

Gnomad4 ASJ exome AF: 0.469

Gnomad4 EAS exome AF: 0.248

Gnomad4 SAS exome AF: 0.398

Gnomad4 FIN exome AF: 0.440

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.412

GnomAD4 genome AF: 0.403 AC: 61326 AN: 152076 Hom.: 12494 Cov.: 32 AF XY: 0.401 AC XY: 29802 AN XY: 74318

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.407

Alfa AF: 0.401 Hom.: 12078

Bravo AF: 0.398

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1010127; hg19: chr5-92226214;