rs10501713

Variant names:

• chr11-90219845-G-A
• rs10501713
• NM_012124.3:c.65-1661C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CHORDC1	NM_012124.3	c.65-1661C>T		intron_variant	Intron 1 of 10	ENST00000320585.11	NP_036256.2
CHORDC1	NM_001144073.2	c.65-1661C>T		intron_variant	Intron 1 of 9		NP_001137545.1
CHORDC1	XM_017017541.3	c.-278-1661C>T		intron_variant	Intron 1 of 10		XP_016873030.1
CHORDC1	XM_047426767.1	c.65-1661C>T		intron_variant	Intron 1 of 7		XP_047282723.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHORDC1	ENST00000320585.11	c.65-1661C>T		intron_variant	Intron 1 of 10	1	NM_012124.3	ENSP00000319255.6

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

African (AFR) AF: 0.0372 AC: 1545 AN: 41524

American (AMR) AF: 0.159 AC: 2429 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3470

East Asian (EAS) AF: 0.0943 AC: 488 AN: 5176

South Asian (SAS) AF: 0.147 AC: 710 AN: 4824

European-Finnish (FIN) AF: 0.179 AC: 1891 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12830 AN: 67990

Other (OTH) AF: 0.158 AC: 333 AN: 2112

Alfa AF: 0.177 Hom.: 1281

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
PhyloP100		-0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10501713; hg19: chr11-89953013;