rs31745

Variant names:

• chr5-141040639-C-T
• rs31745
• ENST00000689319.1:n.267G>A

Variant summary

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

The ENST00000689319.1(PEARL1):​n.267G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,136 control chromosomes in the GnomAD database, including 2,866 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 (2866 hom., cov: 32)
• Consequence: PEARL1 ENST00000689319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 4 publications found

Genes affected

PEARL1 (HGNC:58114):

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000689319.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PEARL1	ENST00000689319.1		n.267G>A		non_coding_transcript_exon	Exon 1 of 1
	PCDHB1-AS1	ENST00000718182.1		n.161-13631G>A		intron	N/A
	PCDHB1-AS1	ENST00000718183.1		n.358-13631G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24350 AN: 152018 Hom.: 2858 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0756

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0788

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0930

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.160 AC: 24396 AN: 152136 Hom.: 2866 Cov.: 32 AF XY: 0.157 AC XY: 11708 AN XY: 74368

African (AFR) AF: 0.334 AC: 13867 AN: 41484

American (AMR) AF: 0.105 AC: 1608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3468

East Asian (EAS) AF: 0.0757 AC: 392 AN: 5176

South Asian (SAS) AF: 0.112 AC: 542 AN: 4824

European-Finnish (FIN) AF: 0.0788 AC: 834 AN: 10578

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6329 AN: 68004

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.123 Hom.: 378

Bravo AF: 0.167

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.71
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs31745; hg19: chr5-140420224;