dbSNP rs823080: PM20D1-AS1:n.233+6569G>A (chr1-205820154-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 ENST00000653632.1(PM20D1-AS1):n.233+6569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,890 control chromosomes in the GnomAD database, including 8,100 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 0.28 ( 8100 hom., cov: 32)

Consequence

PM20D1-AS1
ENST00000653632.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.230

Publications

17 publications found

Variant links:

Genes affected

PM20D1-AS1 (HGNC:27633): (PM20D1 antisense RNA 1)

PM20D1-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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
PM20D1-AS1	ENST00000653632.1 link	n.233+6569G>A	intron_variant	Intron 1 of 4
PM20D1-AS1	ENST00000653838.1 link	n.177+6569G>A	intron_variant	Intron 1 of 4
PM20D1-AS1	ENST00000656162.1 link	n.238+6569G>A	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

43017

AN:

151772

Hom.:

8104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0774

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.00367

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.444

Gnomad MID

AF:

0.332

Gnomad NFE

AF:

0.412

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.283

AC:

43002

AN:

151890

Hom.:

8100

Cov.:

AF XY:

0.278

AC XY:

20673

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.0772

AC:

3198

AN:

41408

American (AMR)

AF:

0.269

AC:

4101

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

1263

AN:

3466

East Asian (EAS)

AF:

0.00367

AC:

AN:

5172

South Asian (SAS)

AF:

0.144

AC:

690

AN:

4804

European-Finnish (FIN)

AF:

0.444

AC:

4673

AN:

10516

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.412

AC:

28001

AN:

67950

Other (OTH)

AF:

0.317

AC:

667

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1364

2728

4093

5457

6821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

426

852

1278

1704

2130

<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:

0.339

Hom.:

1296

Bravo

AF:

0.259

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

(source)

DANN

Benign

0.60

PhyloP100

-0.23

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