rs461951

chr14-60072515-G-T

Variant summary

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

The ENST00000554123.1(PCNX4-DT):n.81+19188C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,086 control chromosomes in the GnomAD database, including 44,644 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 0.75 (44644 hom., cov: 32)
• Consequence: PCNX4-DT ENST00000554123.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

PCNX4-DT (HGNC:55447): (PCNX4 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCNX4-DT	XR_943918.4	n.45-14865C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCNX4-DT	ENST00000554123.1	n.81+19188C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113731 AN: 151968 Hom.: 44636 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.828

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.748 AC: 113766 AN: 152086 Hom.: 44644 Cov.: 32 AF XY: 0.747 AC XY: 55570 AN XY: 74360

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.757

Alfa AF: 0.805 Hom.: 6308

Bravo AF: 0.737

Asia WGS AF: 0.630 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.6
Dann	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs461951; hg19: chr14-60539233;