rs31804

Variant names:

• chr5-141072761-C-T
• rs31804

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 publications found

Genes affected

PCDHB@ (HGNC:8679):

PCDHB1-AS1 (HGNC:56111): (PCDHB1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623109.2. 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
	PCDHB1-AS1	NR_105056.2		n.255+5016G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDHB1-AS1	ENST00000623109.2	TSL:3	n.255+5016G>A		intron	N/A
	PCDHB1-AS1	ENST00000623741.3	TSL:3	n.71-10228G>A		intron	N/A
	PCDHB1-AS1	ENST00000624139.4	TSL:3	n.267+5016G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0248 AC: 3539 AN: 142758 Hom.: 142 Cov.: 29

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.: 29 AF XY: 0.0244 AC XY: 1693 AN XY: 69330

African (AFR) AF: 0.0840 AC: 3329 AN: 39628

American (AMR) AF: 0.0119 AC: 171 AN: 14374

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3348

East Asian (EAS) AF: 0.00 AC: 0 AN: 4200

South Asian (SAS) AF: 0.000249 AC: 1 AN: 4024

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8680

Middle Eastern (MID) AF: 0.00347 AC: 1 AN: 288

European-Non Finnish (NFE) AF: 0.000168 AC: 11 AN: 65466

Other (OTH) AF: 0.0167 AC: 34 AN: 2032

Alfa AF: 0.0218 Hom.: 11

Bravo AF: 0.0266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs31804; hg19: chr5-140452346;