rs10030137

Variant names:

• chr4-30748709-C-T
• rs10030137
• NM_001173523.2:c.3174+24113C>T

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+24113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,204 control chromosomes in the GnomAD database, including 303 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 0.040 (303 hom., cov: 32)
• Consequence: PCDH7 NM_001173523.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCDH7	NM_001173523.2	c.3174+24113C>T		intron_variant	Intron 1 of 2	ENST00000695919.1	NP_001166994.1
PCDH7	NM_032457.4	c.3174+24113C>T		intron_variant	Intron 1 of 2		NP_115833.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCDH7	ENST00000695919.1	c.3174+24113C>T		intron_variant	Intron 1 of 2		NM_001173523.2	ENSP00000512266.1

Frequencies

GnomAD3 genomes AF: 0.0403 AC: 6131 AN: 152086 Hom.: 303 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00933

Gnomad FIN AF: 0.0215

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00829

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0403 AC: 6129 AN: 152204 Hom.: 303 Cov.: 32 AF XY: 0.0392 AC XY: 2915 AN XY: 74422

African (AFR) AF: 0.118 AC: 4892 AN: 41520

American (AMR) AF: 0.0182 AC: 278 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0135 AC: 47 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00913 AC: 44 AN: 4818

European-Finnish (FIN) AF: 0.0215 AC: 228 AN: 10604

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00829 AC: 564 AN: 68010

Other (OTH) AF: 0.0298 AC: 63 AN: 2112

Alfa AF: 0.0211 Hom.: 51

Bravo AF: 0.0444

Asia WGS AF: 0.00866 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.49
PhyloP100		-0.45
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: rs10030137; hg19: chr4-30750331;