dbSNP rs711785: ENSG00000293276:n.887-20478A>G (chr2-173317366-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000809557.1(ENSG00000293276):n.887-20478A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0437 in 152,200 control chromosomes in the GnomAD database, including 163 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 0.044 ( 163 hom., cov: 32)

Consequence

ENSG00000293276
ENST00000809557.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.999

Publications

1 publications found

Variant links:

Genes affected

ENSG00000293276 (HGNC:):

ENSG00000293276 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0527 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
ENSG00000293276	ENST00000809557.1 link	n.887-20478A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0437

AC:

6645

AN:

152082

Hom.:

163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0547

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.0185

Gnomad ASJ

AF:

0.0827

Gnomad EAS

AF:

0.0166

Gnomad SAS

AF:

0.0305

Gnomad FIN

AF:

0.0435

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0437

Gnomad OTH

AF:

0.0354

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

GnomAD4 genome

AF:

0.0437

AC:

6646

AN:

152200

Hom.:

163

Cov.:

AF XY:

0.0429

AC XY:

3195

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0546

AC:

2267

AN:

41528

American (AMR)

AF:

0.0186

AC:

284

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0827

AC:

287

AN:

3470

East Asian (EAS)

AF:

0.0164

AC:

AN:

5184

South Asian (SAS)

AF:

0.0305

AC:

147

AN:

4818

European-Finnish (FIN)

AF:

0.0435

AC:

461

AN:

10596

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0437

AC:

2970

AN:

67998

Other (OTH)

AF:

0.0346

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

313

626

938

1251

1564

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0524

Hom.:

Bravo

AF:

0.0420

Asia WGS

AF:

0.0170

AC:

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

0.45

(source)

DANN

Benign

0.51

PhyloP100

-1.0

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