dbSNP rs9302755: ENSG00000287718:n.408-13316T>G (chr16-51075728-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 ENST00000785664.1(ENSG00000287718):n.408-13316T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,146 control chromosomes in the GnomAD database, including 32,839 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 0.65 ( 32839 hom., cov: 33)

Consequence

ENSG00000287718
ENST00000785664.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.582

Publications

4 publications found

Variant links:

Genes affected

ENSG00000287718 (HGNC:):

ENSG00000287718 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287718	ENST00000785664.1 link	n.408-13316T>G		intron_variant	Intron 2 of 2
ENSG00000287718	ENST00000785665.1 link	n.516+5601T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.649

AC:

98726

AN:

152028

Hom.:

32778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.777

Gnomad AMI

AF:

0.573

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.810

Gnomad SAS

AF:

0.611

Gnomad FIN

AF:

0.538

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.664

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

GnomAD4 genome

AF:

0.650

AC:

98850

AN:

152146

Hom.:

32839

Cov.:

AF XY:

0.648

AC XY:

48199

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.778

AC:

32297

AN:

41524

American (AMR)

AF:

0.648

AC:

9916

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.649

AC:

2253

AN:

3470

East Asian (EAS)

AF:

0.811

AC:

4192

AN:

5172

South Asian (SAS)

AF:

0.611

AC:

2948

AN:

4826

European-Finnish (FIN)

AF:

0.538

AC:

5693

AN:

10572

Middle Eastern (MID)

AF:

0.650

AC:

191

AN:

294

European-Non Finnish (NFE)

AF:

0.580

AC:

39429

AN:

67974

Other (OTH)

AF:

0.667

AC:

1408

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1739

3478

5218

6957

8696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

796

1592

2388

3184

3980

<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:

0.611

Hom.:

123509

Bravo

AF:

0.669

Asia WGS

AF:

0.751

AC:

2616

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.46

(source)

DANN

Benign

0.52

PhyloP100

-0.58

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