4-164725378-G-T

Variant summary

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

The ENST00000506546.1(CHORDC1P3):n.69G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,418 control chromosomes in the GnomAD database, including 286 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 0.053 (285 hom., cov: 32)
  • Exomes 𝑓: 0.054 (1 hom.)
• Consequence: CHORDC1P3 ENST00000506546.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

Genes affected

CHORDC1P3 (HGNC:54689): (CHORDC1 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 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
CHORDC1P3	ENST00000506546.1	n.69G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8058 AN: 152058 Hom.: 284 Cov.: 32

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0560

GnomAD4 exome AF: 0.0537 AC: 13 AN: 242 Hom.: 1 Cov.: 0 AF XY: 0.0455 AC XY: 7 AN XY: 154

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0592

Gnomad4 NFE exome AF: 0.0541

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0530 AC: 8066 AN: 152176 Hom.: 285 Cov.: 32 AF XY: 0.0580 AC XY: 4314 AN XY: 74378

Gnomad4 AFR AF: 0.0341

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0216 Hom.: 10

Bravo AF: 0.0477

Asia WGS AF: 0.114 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.0
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517815; hg19: chr4-165646530;