dbSNP rs3888908: P4HA3-AS1:n.312-213G>A (chr11-74322021-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.75

Publications

11 publications found

Variant links:

Genes affected

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

P4HA3-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 link	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 link	n.312-213G>A		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28710

AN:

151942

Hom.:

2917

Cov.:

show subpopulations

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.:

AF XY:

0.197

AC XY:

14647

AN XY:

74326

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.164

AC:

11156

AN:

67976

Other (OTH)

AF:

0.149

AC:

315

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1175

2349

3524

4698

5873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.96

PhyloP100

2.8

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over