chr11-620599-G-T

Variant names:

• chr11-620599-G-T
• rs7932167
• NM_021924.5:c.790-213C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CDHR5	NM_021924.5	c.790-213C>A		intron_variant	Intron 7 of 14	ENST00000397542.7	NP_068743.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR5	ENST00000397542.7	c.790-213C>A		intron_variant	Intron 7 of 14	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

African (AFR) AF: 0.638 AC: 26444 AN: 41466

American (AMR) AF: 0.698 AC: 10663 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2630 AN: 3468

East Asian (EAS) AF: 0.718 AC: 3701 AN: 5158

South Asian (SAS) AF: 0.687 AC: 3311 AN: 4822

European-Finnish (FIN) AF: 0.810 AC: 8595 AN: 10612

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53077 AN: 67962

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.762 Hom.: 69911

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
PhyloP100		-0.55
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: rs7932167; hg19: chr11-620599;