NM_152750.5:c.2353+605C>T

Variant names:

• chr7-106031445-C-T
• rs17152486
• NM_152750.5:c.2353+605C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_152750.5(CDHR3):​c.2353+605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0151 in 152,232 control chromosomes in the GnomAD database, including 25 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 0.015 (25 hom., cov: 33)
• Consequence: CDHR3 NM_152750.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 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=-0.54).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0151 (2302/152232) while in subpopulation AFR AF = 0.0218 (907/41540). AF 95% confidence interval is 0.0207. There are 25 homozygotes in GnomAd4. There are 1100 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 25 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR3	NM_152750.5	c.2353+605C>T		intron_variant	Intron 18 of 18	ENST00000317716.14	NP_689963.2
CDHR3	NM_001301161.2	c.2089+605C>T		intron_variant	Intron 17 of 17		NP_001288090.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR3	ENST00000317716.14	c.2353+605C>T		intron_variant	Intron 18 of 18	1	NM_152750.5	ENSP00000325954.9

Frequencies

GnomAD3 genomes AF: 0.0151 AC: 2295 AN: 152114 Hom.: 25 Cov.: 33

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.00870

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00748

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0151 AC: 2302 AN: 152232 Hom.: 25 Cov.: 33 AF XY: 0.0148 AC XY: 1100 AN XY: 74410

African (AFR) AF: 0.0218 AC: 907 AN: 41540

American (AMR) AF: 0.00869 AC: 133 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.00748 AC: 36 AN: 4810

European-Finnish (FIN) AF: 0.0169 AC: 179 AN: 10598

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 961 AN: 68018

Other (OTH) AF: 0.0170 AC: 36 AN: 2114

Alfa AF: 0.0135 Hom.: 6

Bravo AF: 0.0149

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.3
DANN	Benign	0.80
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

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: rs17152486; hg19: chr7-105671891;