7-105920689-A-G

Variant names:

• chr7-105920689-A-G
• rs234
• ENST00000470188.5:n.818+8051A>G

Variant summary

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

The ENST00000470188.5(CDHR3):​n.818+8051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,124 control chromosomes in the GnomAD database, including 23,234 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 0.54 (23234 hom., cov: 32)
• Consequence: CDHR3 ENST00000470188.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 11 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000470188.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDHR3	ENST00000470188.5	TSL:2	n.818+8051A>G		intron	N/A
	CDHR3	ENST00000472116.1	TSL:2	n.432+1082A>G		intron	N/A
	CDHR3	ENST00000488386.5	TSL:3	n.-16+43432A>G		intron	N/A	ENSP00000419593.1	F8WF00

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82807 AN: 152006 Hom.: 23192 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.545 AC: 82902 AN: 152124 Hom.: 23234 Cov.: 32 AF XY: 0.549 AC XY: 40813 AN XY: 74382

African (AFR) AF: 0.650 AC: 26961 AN: 41488

American (AMR) AF: 0.610 AC: 9332 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3470

East Asian (EAS) AF: 0.664 AC: 3444 AN: 5188

South Asian (SAS) AF: 0.524 AC: 2524 AN: 4816

European-Finnish (FIN) AF: 0.474 AC: 5023 AN: 10586

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32233 AN: 67960

Other (OTH) AF: 0.558 AC: 1178 AN: 2110

Alfa AF: 0.505 Hom.: 38692

Bravo AF: 0.562

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.9
DANN	Benign	0.81
PhyloP100		0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs234;

hg19: chr7-105561135;