chr4-30787987-G-A

Position:

• chr4-30787987-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001173523.2(PCDH7):​c.3174+63391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,916 control chromosomes in the GnomAD database, including 2,148 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 0.16 (2148 hom., cov: 32)
• Consequence: PCDH7 NM_001173523.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCDH7	NM_001173523.2	c.3174+63391G>A		intron_variant		ENST00000695919.1
PCDH7	NM_032457.4	c.3174+63391G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCDH7	ENST00000695919.1	c.3174+63391G>A		intron_variant			NM_001173523.2	A1
	ENST00000509136.1	n.49-4807C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23984 AN: 151798 Hom.: 2133 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.158 AC: 24027 AN: 151916 Hom.: 2148 Cov.: 32 AF XY: 0.163 AC XY: 12072 AN XY: 74250

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0958 Hom.: 183

Bravo AF: 0.159

Asia WGS AF: 0.258 AC: 897 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374653; hg19: chr4-30789609;