dbSNP rs12191877: ENSG00000298396:n.32+14042C>T (chr6-31285148-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 ENST00000755297.1(ENSG00000298396):n.32+14042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,206 control chromosomes in the GnomAD database, including 1,297 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 0.12 ( 1297 hom., cov: 32)

Consequence

ENSG00000298396
ENST00000755297.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379

Publications

87 publications found

Variant links:

Genes affected

ENSG00000298396 (HGNC:):

ENSG00000298396 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298396	ENST00000755297.1 link	n.32+14042C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18939

AN:

152088

Hom.:

1297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.0534

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.137

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

GnomAD4 genome

AF:

0.124

AC:

18942

AN:

152206

Hom.:

1297

Cov.:

AF XY:

0.125

AC XY:

9286

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.104

AC:

4314

AN:

41520

American (AMR)

AF:

0.110

AC:

1678

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1074

AN:

3468

East Asian (EAS)

AF:

0.0537

AC:

279

AN:

5194

South Asian (SAS)

AF:

0.165

AC:

794

AN:

4822

European-Finnish (FIN)

AF:

0.100

AC:

1062

AN:

10584

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9186

AN:

68012

Other (OTH)

AF:

0.135

AC:

285

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

859

1718

2577

3436

4295

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<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:

0.121

Hom.:

2959

Bravo

AF:

0.124

Asia WGS

AF:

0.0940

AC:

327

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

7.5

(source)

DANN

Benign

0.61

PhyloP100

-0.38

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