rs6444558

Variant names:

• chr3-191557710-C-A
• rs6444558
• ENST00000439804.6:n.203+326C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000439804.6(PYDC2-AS1):​n.203+326C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,928 control chromosomes in the GnomAD database, including 19,690 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 0.49 (19690 hom., cov: 32)
• Consequence: PYDC2-AS1 ENST00000439804.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 1 publications found

Genes affected

PYDC2-AS1 (HGNC:52874): (PYDC2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439804.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYDC2-AS1	NR_120606.1		n.265+326C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYDC2-AS1	ENST00000439804.6	TSL:2	n.203+326C>A		intron	N/A
	PYDC2-AS1	ENST00000641055.1		n.338+326C>A		intron	N/A
	PYDC2-AS1	ENST00000641158.1		n.80-11890C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73587 AN: 151810 Hom.: 19642 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.485 AC: 73693 AN: 151928 Hom.: 19690 Cov.: 32 AF XY: 0.482 AC XY: 35750 AN XY: 74238

African (AFR) AF: 0.726 AC: 30078 AN: 41446

American (AMR) AF: 0.407 AC: 6203 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3472

East Asian (EAS) AF: 0.302 AC: 1557 AN: 5162

South Asian (SAS) AF: 0.496 AC: 2385 AN: 4808

European-Finnish (FIN) AF: 0.381 AC: 4011 AN: 10526

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26779 AN: 67952

Other (OTH) AF: 0.441 AC: 930 AN: 2110

Alfa AF: 0.426 Hom.: 11980

Bravo AF: 0.494

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.44
PhyloP100		-0.0050

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6444558;

hg19: chr3-191275499;