dbSNP rs230487: ENSG00000248161:n.50-18185G>T (chr4-102468252-C-A) – 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.50-18185G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,028 control chromosomes in the GnomAD database, including 39,411 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 0.71 ( 39411 hom., cov: 31)

Consequence

ENSG00000248161
ENST00000843825.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.889

Publications

7 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1 link	n.49-18185G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000843825.1 link	n.50-18185G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.714

AC:

108506

AN:

151908

Hom.:

39346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.790

Gnomad AMI

AF:

0.793

Gnomad AMR

AF:

0.709

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.516

Gnomad FIN

AF:

0.777

Gnomad MID

AF:

0.634

Gnomad NFE

AF:

0.705

Gnomad OTH

AF:

0.676

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

GnomAD4 genome

AF:

0.715

AC:

108628

AN:

152028

Hom.:

39411

Cov.:

AF XY:

0.714

AC XY:

53048

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.790

AC:

32770

AN:

41464

American (AMR)

AF:

0.709

AC:

10837

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

2103

AN:

3470

East Asian (EAS)

AF:

0.379

AC:

1953

AN:

5158

South Asian (SAS)

AF:

0.516

AC:

2481

AN:

4810

European-Finnish (FIN)

AF:

0.777

AC:

8207

AN:

10568

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.705

AC:

47944

AN:

67960

Other (OTH)

AF:

0.672

AC:

1423

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1522

3044

4567

6089

7611

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.698

Hom.:

69246

Bravo

AF:

0.712

Asia WGS

AF:

0.434

AC:

1506

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.62

(source)

DANN

Benign

0.62

PhyloP100

-0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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