dbSNP rs2844615: ENSG00000298396:n.32+4076C>T (chr6-31275182-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+4076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,242 control chromosomes in the GnomAD database, including 1,045 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 ( 1045 hom., cov: 33)

Consequence

ENSG00000298396
ENST00000755297.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85

Publications

7 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 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+4076C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17284

AN:

152122

Hom.:

1044

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.0675

Gnomad FIN

AF:

0.0525

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.121

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

GnomAD4 genome

AF:

0.114

AC:

17284

AN:

152242

Hom.:

1045

Cov.:

AF XY:

0.108

AC XY:

8065

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.112

AC:

4668

AN:

41524

American (AMR)

AF:

0.119

AC:

1818

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

522

AN:

3468

East Asian (EAS)

AF:

0.105

AC:

546

AN:

5182

South Asian (SAS)

AF:

0.0671

AC:

324

AN:

4828

European-Finnish (FIN)

AF:

0.0525

AC:

556

AN:

10596

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.124

AC:

8467

AN:

68022

Other (OTH)

AF:

0.121

AC:

255

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

801

1602

2403

3204

4005

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.118

Hom.:

645

Bravo

AF:

0.120

Asia WGS

AF:

0.0870

AC:

305

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

4.2

(source)

DANN

Benign

0.33

PhyloP100

-1.8

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