dbSNP rs3758947: ENSG00000287898:n.200+2932G>A (chr11-17479663-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 ENST00000662030.2(ENSG00000287898):n.200+2932G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,052 control chromosomes in the GnomAD database, including 2,544 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 0.16 ( 2544 hom., cov: 32)

Consequence

ENSG00000287898
ENST00000662030.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.898

Publications

14 publications found

Variant links:

Genes affected

ENSG00000287898 (HGNC:):

ENSG00000287898 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=-0.77).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902641	XR_007062609.1 link	n.81+2932G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287898	ENST00000662030.2 link	n.200+2932G>A	intron_variant	Intron 1 of 1
ENSG00000287898	ENST00000666786.2 link	n.153+2609G>A	intron_variant	Intron 1 of 1
ENSG00000287898	ENST00000719322.1 link	n.150+3377G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24438

AN:

151934

Hom.:

2546

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0405

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.161

AC:

24434

AN:

152052

Hom.:

2544

Cov.:

AF XY:

0.167

AC XY:

12426

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.0404

AC:

1678

AN:

41508

American (AMR)

AF:

0.272

AC:

4151

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

488

AN:

3472

East Asian (EAS)

AF:

0.266

AC:

1373

AN:

5158

South Asian (SAS)

AF:

0.233

AC:

1123

AN:

4810

European-Finnish (FIN)

AF:

0.245

AC:

2587

AN:

10548

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.185

AC:

12569

AN:

67968

Other (OTH)

AF:

0.132

AC:

278

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

998

1996

2995

3993

4991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.175

Hom.:

4362

Bravo

AF:

0.159

Asia WGS

AF:

0.237

AC:

824

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.1

(source)

DANN

Benign

0.80

PhyloP100

-0.90

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