rs1941817

Variant names:

• chr11-74313775-G-A
• rs1941817
• ENST00000502071.2:n.311+1556G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-74313775-G-A
• chr11-74313775-G-C
• chr11-74313775-G-T

Variant summary

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

The ENST00000502071.2(P4HA3-AS1):​n.311+1556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,080 control chromosomes in the GnomAD database, including 21,923 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 0.53 (21923 hom., cov: 32)
• Consequence: P4HA3-AS1 ENST00000502071.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 7 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502071.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	P4HA3-AS1	NR_120556.1		n.311+1556G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	P4HA3-AS1	ENST00000502071.2	TSL:1	n.311+1556G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81297 AN: 151962 Hom.: 21918 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.535 AC: 81335 AN: 152080 Hom.: 21923 Cov.: 32 AF XY: 0.537 AC XY: 39901 AN XY: 74344

African (AFR) AF: 0.467 AC: 19348 AN: 41474

American (AMR) AF: 0.494 AC: 7551 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1910 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2510 AN: 5162

South Asian (SAS) AF: 0.567 AC: 2734 AN: 4822

European-Finnish (FIN) AF: 0.639 AC: 6760 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38841 AN: 67982

Other (OTH) AF: 0.515 AC: 1086 AN: 2110

Alfa AF: 0.565 Hom.: 19906

Bravo AF: 0.520

Asia WGS AF: 0.521 AC: 1811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.81
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1941817; hg19: chr11-74024820; COSMIC: COSV59043941;