Genetic Variant ENST00000340424.4: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

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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