rs6876364

Variant names:

• chr5-141027409-A-T
• rs6876364
• ENST00000718180.1:n.79-401T>A

Variant summary

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

The ENST00000718180.1(PCDHB1-AS1):​n.79-401T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,180 control chromosomes in the GnomAD database, including 1,448 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 0.13 (1448 hom., cov: 32)
• Consequence: PCDHB1-AS1 ENST00000718180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 3 publications found

Genes affected

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=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718180.1. 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
	PCDHB1-AS1	ENST00000718180.1		n.79-401T>A		intron	N/A
	PCDHB1-AS1	ENST00000718181.1		n.107-401T>A		intron	N/A
	PCDHB1-AS1	ENST00000718182.1		n.161-401T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19097 AN: 152062 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0792

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0924

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19129 AN: 152180 Hom.: 1448 Cov.: 32 AF XY: 0.124 AC XY: 9214 AN XY: 74418

African (AFR) AF: 0.215 AC: 8913 AN: 41490

American (AMR) AF: 0.0909 AC: 1390 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3472

East Asian (EAS) AF: 0.0754 AC: 391 AN: 5184

South Asian (SAS) AF: 0.112 AC: 541 AN: 4824

European-Finnish (FIN) AF: 0.0792 AC: 839 AN: 10594

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0924 AC: 6287 AN: 68018

Other (OTH) AF: 0.116 AC: 245 AN: 2110

Alfa AF: 0.112 Hom.: 135

Bravo AF: 0.128

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.4
DANN	Benign	0.87
PhyloP100		0.094

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6876364;

hg19: chr5-140406994;