ENST00000502071.2:n.312-213G>A

Variant names:

• chr11-74322021-G-A
• rs3888908
• ENST00000502071.2:n.312-213G>A

Variant summary

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

The ENST00000502071.2(P4HA3-AS1):​n.312-213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,060 control chromosomes in the GnomAD database, including 2,920 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 0.19 (2920 hom., cov: 32)
• Consequence: P4HA3-AS1 ENST00000502071.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75
• Publications: 11 publications found

Genes affected

P4HA3-AS1 (HGNC:53160): (P4HA3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
P4HA3-AS1	NR_120556.1	n.312-213G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
P4HA3-AS1	ENST00000502071.2	n.312-213G>A		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28710 AN: 151942 Hom.: 2917 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.189 AC: 28747 AN: 152060 Hom.: 2920 Cov.: 32 AF XY: 0.197 AC XY: 14647 AN XY: 74326

African (AFR) AF: 0.194 AC: 8057 AN: 41498

American (AMR) AF: 0.149 AC: 2277 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1561 AN: 5168

South Asian (SAS) AF: 0.233 AC: 1121 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3594 AN: 10546

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11156 AN: 67976

Other (OTH) AF: 0.149 AC: 315 AN: 2110

Alfa AF: 0.163 Hom.: 5797

Bravo AF: 0.173

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.5
DANN	Benign	0.96
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs3888908; hg19: chr11-74033066;