rs1016618

Variant names:

• chr3-191511201-T-C
• rs1016618
• ENST00000439804.6:n.81-46061T>C

Variant summary

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

The ENST00000439804.6(PYDC2-AS1):​n.81-46061T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,246 control chromosomes in the GnomAD database, including 1,055 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 0.094 (1055 hom., cov: 32)
• Consequence: PYDC2-AS1 ENST00000439804.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.335 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.82-34850T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PYDC2-AS1	ENST00000439804.6	TSL:2	n.81-46061T>C		intron	N/A
	PYDC2-AS1	ENST00000641055.1		n.215+37513T>C		intron	N/A
	PYDC2-AS1	ENST00000641158.1		n.80-58399T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14263 AN: 152128 Hom.: 1053 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.0926

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

GnomAD4 genome AF: 0.0937 AC: 14267 AN: 152246 Hom.: 1055 Cov.: 32 AF XY: 0.0998 AC XY: 7427 AN XY: 74422

African (AFR) AF: 0.0205 AC: 853 AN: 41572

American (AMR) AF: 0.157 AC: 2395 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 543 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1797 AN: 5164

South Asian (SAS) AF: 0.121 AC: 585 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1367 AN: 10590

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6415 AN: 68010

Other (OTH) AF: 0.0945 AC: 200 AN: 2116

Alfa AF: 0.0971 Hom.: 2532

Bravo AF: 0.0934

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.75
PhyloP100		0.61

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: rs1016618;

hg19: chr3-191228990;