6-105158927-G-A

Position:

• chr6-105158927-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000254765.4(POPDC3):​c.595-176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 499,034 control chromosomes in the GnomAD database, including 220,589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.92 (65002 hom., cov: 32)
  • Exomes 𝑓: 0.95 (155587 hom.)
• Consequence: POPDC3 ENST00000254765.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.589

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 6-105158927-G-A is Benign according to our data. Variant chr6-105158927-G-A is described in ClinVar as [Benign]. Clinvar id is 1257854.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POPDC3	NM_022361.5	c.595-176C>T		intron_variant		ENST00000254765.4	NP_071756.2
BVES-AS1	NR_037157.1	n.343-7617G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POPDC3	ENST00000254765.4	c.595-176C>T		intron_variant		1	NM_022361.5	ENSP00000254765	P1
BVES-AS1	ENST00000687937.1	n.342+11547G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140398 AN: 152068 Hom.: 64952 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.927

GnomAD4 exome AF: 0.947 AC: 328423 AN: 346848 Hom.: 155587 Cov.: 4 AF XY: 0.947 AC XY: 169813 AN XY: 179396

Gnomad4 AFR exome AF: 0.852

Gnomad4 AMR exome AF: 0.962

Gnomad4 ASJ exome AF: 0.929

Gnomad4 EAS exome AF: 0.932

Gnomad4 SAS exome AF: 0.927

Gnomad4 FIN exome AF: 0.945

Gnomad4 NFE exome AF: 0.957

Gnomad4 OTH exome AF: 0.941

GnomAD4 genome AF: 0.923 AC: 140507 AN: 152186 Hom.: 65002 Cov.: 32 AF XY: 0.923 AC XY: 68696 AN XY: 74406

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.952

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.927

Alfa AF: 0.935 Hom.: 8280

Bravo AF: 0.920

Asia WGS AF: 0.923 AC: 3209 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.55

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: rs1190283; hg19: chr6-105606802;