4-164725378-G-T

Variant names:

• chr4-164725378-G-T
• rs10517815
• ENST00000506546.1:n.69G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHORDC1P3	ENST00000506546.1	n.69G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.0592 AC: 9 AN: 152

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0541 AC: 4 AN: 74

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.0341 AC: 1418 AN: 41524

American (AMR) AF: 0.0552 AC: 844 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.123 AC: 634 AN: 5166

South Asian (SAS) AF: 0.124 AC: 599 AN: 4822

European-Finnish (FIN) AF: 0.101 AC: 1070 AN: 10582

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0452 AC: 3076 AN: 68008

Other (OTH) AF: 0.0573 AC: 121 AN: 2112

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10517815; hg19: chr4-165646530;