14-89738204-A-G

Variant names:

• chr14-89738204-A-G
• rs10484019
• ENST00000557601.2:n.188T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000557601.2(CHORDC2P):​n.188T>C 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 0.133 in 756,308 control chromosomes in the GnomAD database, including 9,209 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 0.12 (1500 hom., cov: 34)
  • Exomes 𝑓: 0.14 (7709 hom.)
• Consequence: CHORDC2P ENST00000557601.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664
• Publications: 0 publications found

Genes affected

CHORDC2P (HGNC:20050): (cysteine and histidine rich domain containing 2, pseudogene)

ENSG00000259053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557601.2. 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
	CHORDC2P	ENST00000557601.2	TSL:6	n.188T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000259053	ENST00000555070.1	TSL:3	n.170+215702T>C		intron	N/A
	ENSG00000258792	ENST00000819592.1		n.445+33269T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18635 AN: 152118 Hom.: 1496 Cov.: 34

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.136 AC: 81987 AN: 604072 Hom.: 7709 Cov.: 5 AF XY: 0.132 AC XY: 43552 AN XY: 329414

African (AFR) AF: 0.0852 AC: 1459 AN: 17124

American (AMR) AF: 0.141 AC: 5964 AN: 42372

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 1555 AN: 19872

East Asian (EAS) AF: 0.442 AC: 15470 AN: 34964

South Asian (SAS) AF: 0.102 AC: 7105 AN: 69398

European-Finnish (FIN) AF: 0.186 AC: 9311 AN: 50190

Middle Eastern (MID) AF: 0.102 AC: 403 AN: 3954

European-Non Finnish (NFE) AF: 0.109 AC: 36604 AN: 335156

Other (OTH) AF: 0.133 AC: 4116 AN: 31042

GnomAD4 genome AF: 0.123 AC: 18653 AN: 152236 Hom.: 1500 Cov.: 34 AF XY: 0.128 AC XY: 9559 AN XY: 74432

African (AFR) AF: 0.0865 AC: 3594 AN: 41550

American (AMR) AF: 0.147 AC: 2242 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0807 AC: 280 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5154

South Asian (SAS) AF: 0.118 AC: 570 AN: 4832

European-Finnish (FIN) AF: 0.197 AC: 2090 AN: 10602

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7393 AN: 68012

Other (OTH) AF: 0.112 AC: 238 AN: 2116

Alfa AF: 0.0990 Hom.: 125

Bravo AF: 0.117

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.5
DANN	Benign	0.13
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10484019; hg19: chr14-90204548;