dbSNP rs167890: ENSG00000298419:n.439+20031G>A (chr13-110796768-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 ENST00000755406.1(ENSG00000298419):n.439+20031G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 152,002 control chromosomes in the GnomAD database, including 451 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 0.074 ( 451 hom., cov: 30)

Consequence

ENSG00000298419
ENST00000755406.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.747

Publications

4 publications found

Variant links:

Genes affected

ENSG00000298419 (HGNC:):

ENSG00000298419 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000298419	ENST00000755406.1 link	n.439+20031G>A	intron_variant	Intron 2 of 2
ENSG00000298419	ENST00000755407.1 link	n.481+19151G>A	intron_variant	Intron 3 of 3
ENSG00000298419	ENST00000755408.1 link	n.169+19151G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0739

AC:

11223

AN:

151884

Hom.:

448

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0902

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.0553

Gnomad ASJ

AF:

0.0666

Gnomad EAS

AF:

0.0789

Gnomad SAS

AF:

0.0626

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0630

Gnomad OTH

AF:

0.0666

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

GnomAD4 genome

AF:

0.0739

AC:

11239

AN:

152002

Hom.:

451

Cov.:

AF XY:

0.0754

AC XY:

5602

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.0905

AC:

3752

AN:

41444

American (AMR)

AF:

0.0551

AC:

842

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0666

AC:

231

AN:

3470

East Asian (EAS)

AF:

0.0785

AC:

406

AN:

5172

South Asian (SAS)

AF:

0.0627

AC:

302

AN:

4820

European-Finnish (FIN)

AF:

0.111

AC:

1168

AN:

10522

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0630

AC:

4283

AN:

67980

Other (OTH)

AF:

0.0659

AC:

139

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

506

1012

1517

2023

2529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0630

Hom.:

235

Bravo

AF:

0.0709

Asia WGS

AF:

0.0520

AC:

183

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

0.69

(source)

DANN

Benign

0.33

PhyloP100

-0.75

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