6-105176946-G-C

Variant names:

• chr6-105176946-G-C
• rs1190271
• NM_022361.5:c.-252+2887C>G

Variant summary

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

The NM_022361.5(POPDC3):​c.-252+2887C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 162,264 control chromosomes in the GnomAD database, including 43,883 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 (40667 hom., cov: 33)
  • Exomes 𝑓: 0.79 (3216 hom.)
• Consequence: POPDC3 NM_022361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POPDC3	NM_022361.5	c.-252+2887C>G		intron_variant	Intron 1 of 3	ENST00000254765.4	NP_071756.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POPDC3	ENST00000254765.4	c.-252+2887C>G		intron_variant	Intron 1 of 3	1	NM_022361.5	ENSP00000254765.3
POPDC3	ENST00000474760.1	n.163+2887C>G		intron_variant	Intron 1 of 3	2
BVES-AS1	ENST00000687937.1	n.343-22457G>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102729 AN: 152052 Hom.: 40661 Cov.: 33

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.814

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.728

GnomAD4 exome AF: 0.791 AC: 7982 AN: 10096 Hom.: 3216 Cov.: 0 AF XY: 0.788 AC XY: 3938 AN XY: 4996

Gnomad4 AFR exome AF: 0.0991

Gnomad4 AMR exome AF: 0.900

Gnomad4 ASJ exome AF: 0.759

Gnomad4 EAS exome AF: 0.741

Gnomad4 SAS exome AF: 0.759

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.810

Gnomad4 OTH exome AF: 0.782

GnomAD4 genome AF: 0.675 AC: 102739 AN: 152168 Hom.: 40667 Cov.: 33 AF XY: 0.681 AC XY: 50657 AN XY: 74402

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.814

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.848

Gnomad4 OTH AF: 0.730

Alfa AF: 0.742 Hom.: 5486

Bravo AF: 0.652

Asia WGS AF: 0.824 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.73

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: rs1190271; hg19: chr6-105624821;