dbSNP rs230489: ENSG00000248161:n.50-17217A>G (chr4-102467284-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 ENST00000843825.1(ENSG00000248161):n.50-17217A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,256 control chromosomes in the GnomAD database, including 911 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 0.11 ( 911 hom., cov: 32)

Consequence

ENSG00000248161
ENST00000843825.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.228

Publications

9 publications found

Variant links:

Genes affected

ENSG00000248161 (HGNC:58149):

ENSG00000248161 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1 link	n.49-17217A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000843825.1 link	n.50-17217A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

16040

AN:

152138

Hom.:

910

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.0872

Gnomad ASJ

AF:

0.193

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0896

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.105

AC:

16057

AN:

152256

Hom.:

911

Cov.:

AF XY:

0.105

AC XY:

7783

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.117

AC:

4863

AN:

41514

American (AMR)

AF:

0.0871

AC:

1332

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

670

AN:

3470

East Asian (EAS)

AF:

0.000578

AC:

AN:

5190

South Asian (SAS)

AF:

0.0449

AC:

217

AN:

4830

European-Finnish (FIN)

AF:

0.0896

AC:

951

AN:

10608

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7630

AN:

68026

Other (OTH)

AF:

0.114

AC:

240

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

733

1466

2199

2932

3665

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

360

540

720

900

<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:

0.113

Hom.:

2240

Bravo

AF:

0.109

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.0

(source)

DANN

Benign

0.72

PhyloP100

-0.23

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