rs31746

Variant names:

• chr5-141040406-A-G
• rs31746
• ENST00000689319.1:n.500T>C

Variant summary

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

The ENST00000689319.1(ENSG00000288892):​n.500T>C 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 0.397 in 152,000 control chromosomes in the GnomAD database, including 12,795 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 0.40 (12795 hom., cov: 32)
• Consequence: ENSG00000288892 ENST00000689319.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 6 publications found

Genes affected

ENSG00000288892 (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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288892	ENST00000689319.1	n.500T>C		non_coding_transcript_exon_variant	Exon 1 of 1
PCDHB1-AS1	ENST00000718180.1	n.78+70T>C		intron_variant	Intron 1 of 4
PCDHB1-AS1	ENST00000718182.1	n.161-13398T>C		intron_variant	Intron 2 of 4
PCDHB1-AS1	ENST00000718183.1	n.358-13398T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60264 AN: 151882 Hom.: 12764 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.397 AC: 60351 AN: 152000 Hom.: 12795 Cov.: 32 AF XY: 0.396 AC XY: 29444 AN XY: 74312

African (AFR) AF: 0.540 AC: 22373 AN: 41424

American (AMR) AF: 0.389 AC: 5940 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2648 AN: 5168

South Asian (SAS) AF: 0.426 AC: 2053 AN: 4818

European-Finnish (FIN) AF: 0.266 AC: 2811 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22001 AN: 67966

Other (OTH) AF: 0.371 AC: 782 AN: 2106

Alfa AF: 0.351 Hom.: 39285

Bravo AF: 0.412

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.48
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs31746; hg19: chr5-140419991;