chr7-105963785-A-C

Variant names:

• chr7-105963785-A-C
• rs193806
• NM_152750.5:c.46+421A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152750.5(CDHR3):​c.46+421A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,084 control chromosomes in the GnomAD database, including 1,939 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 0.15 (1939 hom., cov: 31)
• Consequence: CDHR3 NM_152750.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 2 publications found

Genes affected

CDHR3 (HGNC:26308): (cadherin related family member 3) Predicted to enable cadherin binding activity and calcium ion binding activity. Predicted to be involved in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell morphogenesis; and cell-cell junction organization. Located in plasma membrane. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR3	NM_152750.5	c.46+421A>C		intron_variant	Intron 1 of 18	ENST00000317716.14	NP_689963.2
CDHR3	NM_001301161.2	c.-16+421A>C		intron_variant	Intron 1 of 17		NP_001288090.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR3	ENST00000317716.14	c.46+421A>C		intron_variant	Intron 1 of 18	1	NM_152750.5	ENSP00000325954.9

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23105 AN: 151964 Hom.: 1937 Cov.: 31

Gnomad AFR AF: 0.0815

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.152 AC: 23124 AN: 152084 Hom.: 1939 Cov.: 31 AF XY: 0.155 AC XY: 11529 AN XY: 74350

African (AFR) AF: 0.0815 AC: 3380 AN: 41482

American (AMR) AF: 0.167 AC: 2545 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1130 AN: 5176

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4812

European-Finnish (FIN) AF: 0.182 AC: 1921 AN: 10574

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11324 AN: 67986

Other (OTH) AF: 0.172 AC: 362 AN: 2108

Alfa AF: 0.160 Hom.: 448

Bravo AF: 0.148

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.072
DANN	Benign	0.68
PhyloP100		-2.0
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: rs193806; hg19: chr7-105604231;