Variant chr5-141072761-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0248 in 142,900 control chromosomes in the GnomAD database, including 143 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 0.025 ( 143 hom., cov: 29)

Consequence

PCDHB@
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Variant links:

Genes affected

PCDHB@ (HGNC:):

PCDHB@ links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCDHB@	use as main transcript	n.141072761C>T		intragenic_variant
PCDHB1-AS1	NR_105056.2 linkuse as main transcript	n.255+5016G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
PCDHB1-AS1	ENST00000623109.1 linkuse as main transcript	n.255+5016G>A	intron_variant	3
PCDHB1-AS1	ENST00000623741.3 linkuse as main transcript	n.71-10228G>A	intron_variant	3
PCDHB1-AS1	ENST00000624778.1 linkuse as main transcript	n.248+5016G>A	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.0248

AC:

3539

AN:

142758

Hom.:

142

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0840

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0119

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000499

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00323

Gnomad NFE

AF:

0.000168

Gnomad OTH

AF:

0.0169

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

GnomAD4 genome

AF:

0.0248

AC:

3547

AN:

142900

Hom.:

143

Cov.:

AF XY:

0.0244

AC XY:

1693

AN XY:

69330

show subpopulations

Gnomad4 AFR

AF:

0.0840

Gnomad4 AMR

AF:

0.0119

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000249

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000168

Gnomad4 OTH

AF:

0.0167

Alfa

AF:

0.0196

Hom.:

Bravo

AF:

0.0266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.4

DANN

Benign

0.77

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over