dbSNP rs2088108: ENSG00000286666:n.222+7024C>T (chr1-233858125-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 ENST00000655369.1(ENSG00000286666):n.222+7024C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,102 control chromosomes in the GnomAD database, including 2,942 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 ( 2942 hom., cov: 32)

Consequence

ENSG00000286666
ENST00000655369.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286666 (HGNC:):

ENSG00000286666 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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286666	ENST00000655369.1 link	n.222+7024C>T	intron_variant	Intron 1 of 1
ENSG00000306050	ENST00000814968.1 link	n.248+10305C>T	intron_variant	Intron 1 of 4
ENSG00000286666	ENST00000815093.1 link	n.531-334C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26705

AN:

151984

Hom.:

2925

Cov.:

show subpopulations

Gnomad AFR

AF:

0.314

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.159

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.161

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

GnomAD4 genome

AF:

0.176

AC:

26763

AN:

152102

Hom.:

2942

Cov.:

AF XY:

0.174

AC XY:

12926

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.315

AC:

13056

AN:

41472

American (AMR)

AF:

0.112

AC:

1708

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

529

AN:

3472

East Asian (EAS)

AF:

0.226

AC:

1170

AN:

5178

South Asian (SAS)

AF:

0.160

AC:

770

AN:

4810

European-Finnish (FIN)

AF:

0.103

AC:

1087

AN:

10578

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.116

AC:

7917

AN:

68000

Other (OTH)

AF:

0.165

AC:

348

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1072

2144

3215

4287

5359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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.:

6424

Bravo

AF:

0.184

Asia WGS

AF:

0.223

AC:

773

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.1

(source)

DANN

Benign

0.73

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