rs11962089

Positions:

• chr6-105164345-A-G

Variant summary

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

The NM_022361.5(POPDC3):​c.-251-2185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,192 control chromosomes in the GnomAD database, including 2,783 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 (2783 hom., cov: 32)
• Consequence: POPDC3 NM_022361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POPDC3	NM_022361.5	c.-251-2185T>C		intron_variant		ENST00000254765.4	NP_071756.2
BVES-AS1	NR_037157.1	n.343-2199A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POPDC3	ENST00000254765.4	c.-251-2185T>C		intron_variant		1	NM_022361.5	ENSP00000254765	P1
BVES-AS1	ENST00000687937.1	n.342+16965A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24541 AN: 152074 Hom.: 2763 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.162 AC: 24608 AN: 152192 Hom.: 2783 Cov.: 32 AF XY: 0.159 AC XY: 11842 AN XY: 74426

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.0301

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.142

Alfa AF: 0.111 Hom.: 2276

Bravo AF: 0.171

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11962089; hg19: chr6-105612220;