dbSNP rs299247: ENSG00000266850:n.288-4889G>A (chr18-22709809-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000578831.1(ENSG00000266850):n.288-4889G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,108 control chromosomes in the GnomAD database, including 6,417 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 0.24 ( 6417 hom., cov: 32)

Consequence

ENSG00000266850
ENST00000578831.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.196

Publications

6 publications found

Variant links:

Genes affected

ENSG00000266850 (HGNC:58091):

ENSG00000266850 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000266850	ENST00000578831.1 link	n.288-4889G>A	intron_variant	Intron 2 of 3	4
ENSG00000266850	ENST00000716263.1 link	n.536-4889G>A	intron_variant	Intron 3 of 6
ENSG00000266850	ENST00000716264.1 link	n.436-4889G>A	intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36302

AN:

151988

Hom.:

6387

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.0750

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.120

Gnomad OTH

AF:

0.202

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

GnomAD4 genome

AF:

0.239

AC:

36385

AN:

152108

Hom.:

6417

Cov.:

AF XY:

0.238

AC XY:

17729

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.483

AC:

20007

AN:

41442

American (AMR)

AF:

0.207

AC:

3156

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

370

AN:

3468

East Asian (EAS)

AF:

0.372

AC:

1919

AN:

5160

South Asian (SAS)

AF:

0.286

AC:

1379

AN:

4818

European-Finnish (FIN)

AF:

0.0750

AC:

796

AN:

10610

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.120

AC:

8168

AN:

68012

Other (OTH)

AF:

0.206

AC:

435

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1190

2381

3571

4762

5952

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

352

704

1056

1408

1760

<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:

0.153

Hom.:

4017

Bravo

AF:

0.258

Asia WGS

AF:

0.363

AC:

1265

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

0.20

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