rs4074485

Variant names:

• chr3-191571662-C-G
• rs4074485
• ENST00000438488.1:n.299-1652C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-191571662-C-G
• chr3-191571662-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000438488.1(PYDC2-AS1):​n.299-1652C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: PYDC2-AS1 ENST00000438488.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYDC2-AS1	NR_120606.1	n.568-1652C>G		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYDC2-AS1	ENST00000438488.1	n.299-1652C>G		intron_variant	Intron 2 of 2	5
PYDC2-AS1	ENST00000439804.6	n.429-1652C>G		intron_variant	Intron 3 of 4	2
PYDC2-AS1	ENST00000641055.1	n.637-1652C>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs4074485; hg19: chr3-191289451;