rs1010127

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr5-92890507-A-G
• chr5-92890507-A-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000479109.2. 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
	CCT7P2	ENST00000479109.2	TSL:6	n.334T>C		non_coding_transcript_exon	Exon 1 of 1
	LINC02058	ENST00000766746.1		n.241-1912T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1010127;

hg19: chr5-92226214;