Genetic Variant SIRPB3P:n.73-3184T>A (chr20-1700963-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000340424.4(SIRPB3P):n.73-3184T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 151,650 control chromosomes in the GnomAD database, including 2,836 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 0.17 ( 2836 hom., cov: 31)

Consequence

SIRPB3P
ENST00000340424.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.292

Publications

1 publications found

Variant links:

Genes affected

SIRPB3P (HGNC:49209): (signal regulatory protein beta 3, pseudogene)

SIRPB3P links:

ENSG00000286288 (HGNC:):

ENSG00000286288 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIRPB3P	NR_164369.1 link	n.254+669T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIRPB3P	ENST00000340424.4 link	n.73-3184T>A		intron_variant	Intron 1 of 4	6
ENSG00000286288	ENST00000844954.1 link	n.700-3184T>A		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25379

AN:

151532

Hom.:

2832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.0584

Gnomad AMR

AF:

0.0983

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.000967

Gnomad SAS

AF:

0.0409

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.140

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

GnomAD4 genome

AF:

0.168

AC:

25416

AN:

151650

Hom.:

2836

Cov.:

AF XY:

0.163

AC XY:

12071

AN XY:

74110

show subpopulations

African (AFR)

AF:

0.318

AC:

13138

AN:

41252

American (AMR)

AF:

0.0981

AC:

1495

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.139

AC:

482

AN:

3466

East Asian (EAS)

AF:

0.000970

AC:

AN:

5156

South Asian (SAS)

AF:

0.0409

AC:

196

AN:

4790

European-Finnish (FIN)

AF:

0.116

AC:

1218

AN:

10508

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.125

AC:

8497

AN:

67930

Other (OTH)

AF:

0.139

AC:

293

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1004

2008

3013

4017

5021

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.0680

Hom.:

Bravo

AF:

0.172

Asia WGS

AF:

0.0420

AC:

149

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.31

PhyloP100

-0.29

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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