6-105161325-C-T

Position:

• chr6-105161325-C-T

Variant summary

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

The ENST00000254765.4(POPDC3):​c.485+100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00503 in 1,363,476 control chromosomes in the GnomAD database, including 187 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.020 (97 hom., cov: 33)
  • Exomes 𝑓: 0.0032 (90 hom.)
• Consequence: POPDC3 ENST00000254765.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.266

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=-0.7).
• BP6: Variant 6-105161325-C-T is Benign according to our data. Variant chr6-105161325-C-T is described in ClinVar as [Benign]. Clinvar id is 1265554.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POPDC3	NM_022361.5	c.485+100G>A		intron_variant		ENST00000254765.4	NP_071756.2
BVES-AS1	NR_037157.1	n.343-5219C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POPDC3	ENST00000254765.4	c.485+100G>A		intron_variant		1	NM_022361.5	ENSP00000254765	P1
BVES-AS1	ENST00000687937.1	n.342+13945C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0198 AC: 3015 AN: 152080 Hom.: 96 Cov.: 33

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00931

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.0278

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000235

Gnomad OTH AF: 0.0144

GnomAD4 exome AF: 0.00317 AC: 3845 AN: 1211278 Hom.: 90 AF XY: 0.00293 AC XY: 1762 AN XY: 600422

Gnomad4 AFR exome AF: 0.0669

Gnomad4 AMR exome AF: 0.00478

Gnomad4 ASJ exome AF: 0.00662

Gnomad4 EAS exome AF: 0.0304

Gnomad4 SAS exome AF: 0.000754

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000180

Gnomad4 OTH exome AF: 0.00695

GnomAD4 genome AF: 0.0198 AC: 3020 AN: 152198 Hom.: 97 Cov.: 33 AF XY: 0.0196 AC XY: 1455 AN XY: 74414

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.00929

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.0276

Gnomad4 SAS AF: 0.00166

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000235

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0134 Hom.: 2

Bravo AF: 0.0224

Asia WGS AF: 0.0120 AC: 43 AN: 3478

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 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.64

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: rs78510188; hg19: chr6-105609200;