chr6-105176540-T-G

Position:

• chr6-105176540-T-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+3293A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 151,936 control chromosomes in the GnomAD database, including 52,957 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 0.82 (52957 hom., cov: 32)
• Consequence: POPDC3 NM_022361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POPDC3	NM_022361.5	c.-252+3293A>C		intron_variant		ENST00000254765.4	NP_071756.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POPDC3	ENST00000254765.4	c.-252+3293A>C		intron_variant		1	NM_022361.5	ENSP00000254765	P1
BVES-AS1	ENST00000687937.1	n.343-22863T>G		intron_variant, non_coding_transcript_variant
POPDC3	ENST00000474760.1	n.163+3293A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124483 AN: 151818 Hom.: 52928 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.820 AC: 124552 AN: 151936 Hom.: 52957 Cov.: 32 AF XY: 0.823 AC XY: 61100 AN XY: 74264

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.899

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.854

Alfa AF: 0.906 Hom.: 75443

Bravo AF: 0.808

Asia WGS AF: 0.887 AC: 3087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.77

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: rs1190270; hg19: chr6-105624415;