Genetic Variant ASNSP1:n.552+18208T>G (chr8-46620127-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000641977.1(ASNSP1):n.552+18208T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,988 control chromosomes in the GnomAD database, including 21,652 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 0.48 ( 21652 hom., cov: 33)

Consequence

ASNSP1
ENST00000641977.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.734

Publications

2 publications found

Variant links:

Genes affected

ASNSP1 (HGNC:):

ASNSP1 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ASNSP1	ENST00000641977.1 link	n.552+18208T>G	intron_variant	Intron 1 of 6
ENSG00000302462	ENST00000787002.1 link	n.132+2566A>C	intron_variant	Intron 1 of 3
ENSG00000302462	ENST00000787006.1 link	n.126+2566A>C	intron_variant	Intron 1 of 2
ENSG00000302462	ENST00000787007.1 link	n.125+2566A>C	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73170

AN:

151870

Hom.:

21653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.675

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.595

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.663

Gnomad OTH

AF:

0.506

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

GnomAD4 genome

AF:

0.481

AC:

73156

AN:

151988

Hom.:

21652

Cov.:

AF XY:

0.478

AC XY:

35484

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.125

AC:

5193

AN:

41428

American (AMR)

AF:

0.535

AC:

8170

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.545

AC:

1893

AN:

3472

East Asian (EAS)

AF:

0.561

AC:

2886

AN:

5140

South Asian (SAS)

AF:

0.383

AC:

1850

AN:

4824

European-Finnish (FIN)

AF:

0.595

AC:

6292

AN:

10572

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.663

AC:

45055

AN:

67970

Other (OTH)

AF:

0.501

AC:

1060

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.528

Heterozygous variant carriers

1358

2716

4073

5431

6789

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<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:

0.565

Hom.:

11467

Bravo

AF:

0.461

Asia WGS

AF:

0.403

AC:

1405

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.1

(source)

DANN

Benign

0.49

PhyloP100

-0.73

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