rs199796910

Variant names:

• chr10-71682505-C-A
• NM_022124.6:c.1919C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-71682505-C-A
• chr10-71682505-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_022124.6(CDH23):​c.1919C>A​(p.Thr640Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,050 control chromosomes in the GnomAD database, with no homozygous occurrence. 10/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T640M) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CDH23 NM_022124.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20

Genes affected

CDH23 (HGNC:13733): (cadherin related 23) This gene is a member of the cadherin superfamily, whose genes encode calcium dependent cell-cell adhesion glycoproteins. The encoded protein is thought to be involved in stereocilia organization and hair bundle formation. The gene is located in a region containing the human deafness loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this cadherin-like gene. Upregulation of this gene may also be associated with breast cancer. Alternative splice variants encoding different isoforms have been described. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDH23	NM_022124.6	c.1919C>A	p.Thr640Lys	missense_variant	Exon 18 of 70	ENST00000224721.12	NP_071407.4
CDH23	NM_001171930.2	c.1919C>A	p.Thr640Lys	missense_variant	Exon 18 of 32		NP_001165401.1
CDH23	NM_001171931.2	c.1919C>A	p.Thr640Lys	missense_variant	Exon 18 of 26		NP_001165402.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDH23	ENST00000224721.12	c.1919C>A	p.Thr640Lys	missense_variant	Exon 18 of 70	5	NM_022124.6	ENSP00000224721.9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461050 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726704

Gnomad4 AFR exome AF: 0.0000299

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: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
CADD	Benign	10
DANN	Benign	0.96
DEOGEN2	Benign	0.064	T;T;T;.;T;.
Eigen	Benign	-0.46
Eigen_PC	Benign	-0.48
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.90	D;D;D;D;D;D
M_CAP	Benign	0.015	T
MetaRNN	Uncertain	0.64	D;D;D;D;D;D
MetaSVM	Benign	-0.73	T
MutationAssessor	Benign	1.5	.;.;L;.;.;.
PrimateAI	Uncertain	0.48	T
REVEL	Benign	0.26
Sift4G	Uncertain	0.030	D;D;.;T;D;.
Polyphen		0.23	.;.;B;.;.;.
Vest4		0.74
MutPred		0.68		Gain of ubiquitination at T640 (P = 0.0276);Gain of ubiquitination at T640 (P = 0.0276);Gain of ubiquitination at T640 (P = 0.0276);Gain of ubiquitination at T640 (P = 0.0276);Gain of ubiquitination at T640 (P = 0.0276);Gain of ubiquitination at T640 (P = 0.0276);
MVP		0.63
ClinPred		0.90	D
GERP RS		2.5
Varity_R		0.14
gMVP		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-73442262;