chr4-133145551-C-T

Variant names:

• chr4-133145551-C-T
• rs3811831
• ENST00000505289.6:n.306+53G>A

Variant summary

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

The ENST00000505289.6(PCDH10-DT):​n.306+53G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.026 in 152,054 control chromosomes in the GnomAD database, including 92 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 0.026 (92 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: PCDH10-DT ENST00000505289.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 1 publications found

Genes affected

PCDH10-DT (HGNC:53036): (PCDH10 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505289.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH10-DT	NR_125885.1		n.308+53G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDH10-DT	ENST00000505289.6	TSL:1	n.306+53G>A		intron	N/A
	PCDH10-DT	ENST00000509715.1	TSL:4	n.308+53G>A		intron	N/A
	PCDH10-DT	ENST00000656167.1		n.305+53G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3942 AN: 151936 Hom.: 89 Cov.: 31

Gnomad AFR AF: 0.0155

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0461

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.0731

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0150

Gnomad OTH AF: 0.0230

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

GnomAD4 genome AF: 0.0260 AC: 3959 AN: 152054 Hom.: 92 Cov.: 31 AF XY: 0.0292 AC XY: 2172 AN XY: 74322

African (AFR) AF: 0.0157 AC: 651 AN: 41502

American (AMR) AF: 0.0462 AC: 706 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3468

East Asian (EAS) AF: 0.127 AC: 655 AN: 5142

South Asian (SAS) AF: 0.0733 AC: 352 AN: 4800

European-Finnish (FIN) AF: 0.0428 AC: 453 AN: 10588

Middle Eastern (MID) AF: 0.0137 AC: 4 AN: 292

European-Non Finnish (NFE) AF: 0.0150 AC: 1019 AN: 67978

Other (OTH) AF: 0.0237 AC: 50 AN: 2106

Alfa AF: 0.0210 Hom.: 48

Bravo AF: 0.0264

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.50
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs3811831; hg19: chr4-134066706;