dbSNP rs1884390: ENSG00000296607:n.124+4784A>G (chr20-1430174-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 ENST00000740734.1(ENSG00000296607):n.124+4784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,144 control chromosomes in the GnomAD database, including 1,782 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 0.14 ( 1782 hom., cov: 32)

Consequence

ENSG00000296607
ENST00000740734.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.308

Publications

2 publications found

Variant links:

Genes affected

ENSG00000296607 (HGNC:):

ENSG00000296607 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.218 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
ENSG00000296607	ENST00000740734.1 link	n.124+4784A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.140

AC:

21254

AN:

152026

Hom.:

1783

Cov.:

show subpopulations

Gnomad AFR

AF:

0.222

Gnomad AMI

AF:

0.0451

Gnomad AMR

AF:

0.0963

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.00695

Gnomad SAS

AF:

0.152

Gnomad FIN

AF:

0.0741

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.118

Gnomad OTH

AF:

0.148

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

GnomAD4 genome

AF:

0.140

AC:

21281

AN:

152144

Hom.:

1782

Cov.:

AF XY:

0.137

AC XY:

10213

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.222

AC:

9194

AN:

41464

American (AMR)

AF:

0.0961

AC:

1470

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3470

East Asian (EAS)

AF:

0.00716

AC:

AN:

5166

South Asian (SAS)

AF:

0.154

AC:

741

AN:

4820

European-Finnish (FIN)

AF:

0.0741

AC:

786

AN:

10608

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.118

AC:

8043

AN:

68012

Other (OTH)

AF:

0.149

AC:

315

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

883

1766

2650

3533

4416

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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:

0.135

Hom.:

192

Bravo

AF:

0.144

Asia WGS

AF:

0.0850

AC:

295

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.74

PhyloP100

0.31

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