11-620599-G-T

Position:

• chr11-620599-G-T

Variant summary

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

The NM_021924.5(CDHR5):​c.790-213C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,086 control chromosomes in the GnomAD database, including 40,763 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 0.73 (40763 hom., cov: 33)
• Consequence: CDHR5 NM_021924.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

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]

CDHR5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDHR5	NM_021924.5	c.790-213C>A		intron_variant		ENST00000397542.7	NP_068743.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDHR5	ENST00000397542.7	c.790-213C>A		intron_variant		1	NM_021924.5	ENSP00000380676.2

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110916 AN: 151968 Hom.: 40765 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.730 AC: 110948 AN: 152086 Hom.: 40763 Cov.: 33 AF XY: 0.728 AC XY: 54130 AN XY: 74346

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.746

Alfa AF: 0.766 Hom.: 54813

Bravo AF: 0.720

Asia WGS AF: 0.671 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.40

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: rs7932167; hg19: chr11-620599;