NM_001173523.2:c.3174+47865C>A

Variant names:

• chr4-30772461-C-A
• rs10517215
• NM_001173523.2:c.3174+47865C>A

Variant summary

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

The NM_001173523.2(PCDH7):​c.3174+47865C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,092 control chromosomes in the GnomAD database, including 1,718 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 0.14 (1718 hom., cov: 32)
• Consequence: PCDH7 NM_001173523.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 4 publications found

Genes affected

PCDH7 (HGNC:8659): (protocadherin 7) This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes a protein with an extracellular domain containing 7 cadherin repeats. The gene product is an integral membrane protein that is thought to function in cell-cell recognition and adhesion. Alternative splicing yields isoforms with unique cytoplasmic tails. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001173523.2. 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
	PCDH7	NM_001173523.2	MANE Select	c.3174+47865C>A		intron	N/A	NP_001166994.1	A0A8Q3SI70
	PCDH7	NM_032457.4		c.3174+47865C>A		intron	N/A	NP_115833.2	A0A8V8TM73

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH7	ENST00000695919.1	MANE Select	c.3174+47865C>A		intron	N/A	ENSP00000512266.1	A0A8Q3SI70
	PCDH7	ENST00000621961.2	TSL:5	c.3174+47865C>A		intron	N/A	ENSP00000484874.2	A0A087X2C4
	PCDH7	ENST00000946629.1		c.3175-14266C>A		intron	N/A	ENSP00000616688.1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21284 AN: 151974 Hom.: 1708 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.140 AC: 21299 AN: 152092 Hom.: 1718 Cov.: 32 AF XY: 0.145 AC XY: 10748 AN XY: 74346

African (AFR) AF: 0.106 AC: 4407 AN: 41518

American (AMR) AF: 0.173 AC: 2635 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1519 AN: 5164

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4814

European-Finnish (FIN) AF: 0.127 AC: 1339 AN: 10576

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9440 AN: 67974

Other (OTH) AF: 0.125 AC: 263 AN: 2104

Alfa AF: 0.141 Hom.: 837

Bravo AF: 0.140

Asia WGS AF: 0.243 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.027
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10517215; hg19: chr4-30774083;