ENST00000479109.2:n.334T>C

Variant names:

• chr5-92890507-A-G
• rs1010127
• ENST00000479109.2:n.334T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

LINC02058 (HGNC:52901): (long intergenic non-protein coding RNA 2058)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCT7P2		n.92890507A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCT7P2	ENST00000479109.2	n.334T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02058	ENST00000766746.1	n.241-1912T>C		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.459 AC: 5648 AN: 12308

American (AMR) AF: 0.350 AC: 8348 AN: 23874

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 6341 AN: 13522

East Asian (EAS) AF: 0.248 AC: 6015 AN: 24226

South Asian (SAS) AF: 0.398 AC: 20953 AN: 52668

European-Finnish (FIN) AF: 0.440 AC: 18370 AN: 41748

Middle Eastern (MID) AF: 0.426 AC: 818 AN: 1922

European-Non Finnish (NFE) AF: 0.421 AC: 105966 AN: 251444

Other (OTH) AF: 0.412 AC: 9801 AN: 23762

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

African (AFR) AF: 0.434 AC: 17998 AN: 41504

American (AMR) AF: 0.350 AC: 5345 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1065 AN: 5144

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4820

European-Finnish (FIN) AF: 0.418 AC: 4425 AN: 10584

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27768 AN: 67976

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.401 Hom.: 17843

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
PhyloP100		4.1

Splicing

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

Other links and lift over

dbSNP: rs1010127; hg19: chr5-92226214;