rs10501713

chr11-90219845-G-A

Variant summary

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

The NM_012124.3(CHORDC1):c.65-1661C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,168 control chromosomes in the GnomAD database, including 1,818 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 0.14 (1818 hom., cov: 32)
• Consequence: CHORDC1 NM_012124.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

CHORDC1 (HGNC:14525): (cysteine and histidine rich domain containing 1) Enables Hsp90 protein binding activity. Predicted to be involved in centrosome duplication; chaperone-mediated protein folding; and regulation of cellular response to heat. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHORDC1	NM_012124.3	c.65-1661C>T		intron_variant		ENST00000320585.11
CHORDC1	NM_001144073.2	c.65-1661C>T		intron_variant
CHORDC1	XM_017017541.3	c.-278-1661C>T		intron_variant
CHORDC1	XM_047426767.1	c.65-1661C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHORDC1	ENST00000320585.11	c.65-1661C>T		intron_variant		1	NM_012124.3	P1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21003 AN: 152050 Hom.: 1819 Cov.: 32

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.157

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.138 AC: 21002 AN: 152168 Hom.: 1818 Cov.: 32 AF XY: 0.139 AC XY: 10366 AN XY: 74398

Gnomad4 AFR AF: 0.0372

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0943

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.158

Alfa AF: 0.175 Hom.: 1121

Bravo AF: 0.134

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.81
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501713; hg19: chr11-89953013;