chr5-141042553-T-C

Variant names:

• chr5-141042553-T-C
• rs17119385
• ENST00000718182.1:n.161-15545A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000718182.1(PCDHB1-AS1):​n.161-15545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,170 control chromosomes in the GnomAD database, including 1,118 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 0.11 (1118 hom., cov: 32)
• Consequence: PCDHB1-AS1 ENST00000718182.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718182.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCDHB1-AS1	ENST00000718182.1		n.161-15545A>G		intron	N/A
	PCDHB1-AS1	ENST00000718183.1		n.358-15545A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16597 AN: 152054 Hom.: 1118 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0814

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.109 AC: 16620 AN: 152170 Hom.: 1118 Cov.: 32 AF XY: 0.108 AC XY: 8031 AN XY: 74418

African (AFR) AF: 0.190 AC: 7879 AN: 41494

American (AMR) AF: 0.0761 AC: 1164 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0814 AC: 282 AN: 3466

East Asian (EAS) AF: 0.0755 AC: 391 AN: 5178

South Asian (SAS) AF: 0.111 AC: 534 AN: 4822

European-Finnish (FIN) AF: 0.0730 AC: 774 AN: 10606

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0771 AC: 5242 AN: 67990

Other (OTH) AF: 0.102 AC: 216 AN: 2110

Alfa AF: 0.0503 Hom.: 60

Bravo AF: 0.111

Asia WGS AF: 0.0990 AC: 342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	5.1
DANN	Benign	0.77
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs17119385; hg19: chr5-140422138;