chr6-105163071-C-T

Variant names:

• chr6-105163071-C-T
• rs1190286
• NM_022361.5:c.-251-911G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
POPDC3	NM_022361.5	c.-251-911G>A		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.-251-911G>A		intron_variant	Intron 1 of 3	1	NM_022361.5	ENSP00000254765.3

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

African (AFR) AF: 0.223 AC: 9259 AN: 41432

American (AMR) AF: 0.814 AC: 12429 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2862 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4537 AN: 5170

South Asian (SAS) AF: 0.822 AC: 3962 AN: 4818

European-Finnish (FIN) AF: 0.878 AC: 9288 AN: 10576

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.848 AC: 57695 AN: 68006

Other (OTH) AF: 0.730 AC: 1541 AN: 2112

Alfa AF: 0.794 Hom.: 62104

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1190286; hg19: chr6-105610946;