11-625695-G-A

Position:

• chr11-625695-G-A

Variant summary

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

The ENST00000674088.1(CDHR5):​c.-266+326C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,082 control chromosomes in the GnomAD database, including 4,371 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 0.23 (4371 hom., cov: 32)
• Consequence: CDHR5 ENST00000674088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

Genes affected

CDHR5 (HGNC:7521): (cadherin related family member 5) This gene is a novel mucin-like gene that is a member of the cadherin superfamily. While encoding nonpolymorphic tandem repeats rich in proline, serine and threonine similar to mucin proteins, the gene also contains sequence encoding calcium-binding motifs found in all cadherins. The role of the hybrid extracellular region and the specific function of this protein have not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDHR5	ENST00000674088.1	c.-266+326C>T		intron_variant				P2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35219 AN: 151964 Hom.: 4370 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0249

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.232 AC: 35232 AN: 152082 Hom.: 4371 Cov.: 32 AF XY: 0.223 AC XY: 16603 AN XY: 74354

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0250

Gnomad4 SAS AF: 0.0957

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.233

Alfa AF: 0.237 Hom.: 554

Bravo AF: 0.243

Asia WGS AF: 0.0910 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35134589; hg19: chr11-625695;