dbSNP rs2110483: ENSG00000285090:n.365-16555A>G (chr7-94250781-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 ENST00000834100.1(ENSG00000285090):n.365-16555A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,956 control chromosomes in the GnomAD database, including 4,592 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 0.18 ( 4592 hom., cov: 32)

Consequence

ENSG00000285090
ENST00000834100.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.938

Publications

1 publications found

Variant links:

Genes affected

ENSG00000285090 (HGNC:):

ENSG00000285090 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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
ENSG00000285090	ENST00000834100.1 link	n.365-16555A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.177

AC:

26929

AN:

151838

Hom.:

4573

Cov.:

show subpopulations

Gnomad AFR

AF:

0.450

Gnomad AMI

AF:

0.107

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.0870

Gnomad EAS

AF:

0.0455

Gnomad SAS

AF:

0.0723

Gnomad FIN

AF:

0.0270

Gnomad MID

AF:

0.153

Gnomad NFE

AF:

0.0637

Gnomad OTH

AF:

0.164

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

GnomAD4 genome

AF:

0.178

AC:

26994

AN:

151956

Hom.:

4592

Cov.:

AF XY:

0.172

AC XY:

12748

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.451

AC:

18641

AN:

41364

American (AMR)

AF:

0.155

AC:

2358

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.0870

AC:

301

AN:

3460

East Asian (EAS)

AF:

0.0455

AC:

235

AN:

5170

South Asian (SAS)

AF:

0.0726

AC:

350

AN:

4822

European-Finnish (FIN)

AF:

0.0270

AC:

286

AN:

10594

Middle Eastern (MID)

AF:

0.168

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0637

AC:

4333

AN:

67974

Other (OTH)

AF:

0.163

AC:

343

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

893

1786

2680

3573

4466

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.130

Hom.:

1078

Bravo

AF:

0.202

Asia WGS

AF:

0.0970

AC:

339

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.55

(source)

DANN

Benign

0.45

PhyloP100

-0.94

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