rs1190286

chr6-105163071-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022361.5(POPDC3):c.-251-911G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,068 control chromosomes in the GnomAD database, including 40,622 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 0.68 (40622 hom., cov: 31)
• Consequence: POPDC3 NM_022361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

POPDC3 (HGNC:17649): (popeye domain containing 3) This gene encodes a member of the POP family of proteins containing three putative transmembrane domains. This gene is expressed in cardiac and skeletal muscle and may play an important role in these tissues during development. Alternatively spliced transcript variants have been found. [provided by RefSeq, Nov 2008]

BVES-AS1 (HGNC:21223): (BVES antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POPDC3	NM_022361.5	c.-251-911G>A		intron_variant		ENST00000254765.4
BVES-AS1	NR_037157.1	n.343-3473C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POPDC3	ENST00000254765.4	c.-251-911G>A		intron_variant		1	NM_022361.5	P1
BVES-AS1	ENST00000687937.1	n.342+15691C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102638 AN: 151952 Hom.: 40617 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.675 AC: 102647 AN: 152068 Hom.: 40622 Cov.: 31 AF XY: 0.681 AC XY: 50602 AN XY: 74336

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.730

Alfa AF: 0.814 Hom.: 50142

Bravo AF: 0.652

Asia WGS AF: 0.823 AC: 2862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.75
Dann	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1190286; hg19: chr6-105610946;