dbSNP rs6140378: ENSG00000309276:n.397-5293G>T (chr20-7674292-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 ENST00000839999.1(ENSG00000309276):n.397-5293G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,096 control chromosomes in the GnomAD database, including 2,994 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 0.17 ( 2994 hom., cov: 33)

Consequence

ENSG00000309276
ENST00000839999.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.607

Publications

4 publications found

Variant links:

Genes affected

ENSG00000309276 (HGNC:):

ENSG00000309276 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 (EAS) allele frequency at 95% confidence interval = 0.594 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
ENSG00000309276	ENST00000839999.1 link	n.397-5293G>T		intron_variant	Intron 3 of 4
ENSG00000309276	ENST00000840000.1 link	n.76-5293G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26495

AN:

151976

Hom.:

2995

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.0928

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.175

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

GnomAD4 genome

AF:

0.174

AC:

26512

AN:

152096

Hom.:

2994

Cov.:

AF XY:

0.176

AC XY:

13096

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.190

AC:

7900

AN:

41482

American (AMR)

AF:

0.145

AC:

2214

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

504

AN:

3470

East Asian (EAS)

AF:

0.612

AC:

3158

AN:

5162

South Asian (SAS)

AF:

0.355

AC:

1710

AN:

4816

European-Finnish (FIN)

AF:

0.0928

AC:

983

AN:

10590

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.138

AC:

9401

AN:

67992

Other (OTH)

AF:

0.182

AC:

385

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1068

2135

3203

4270

5338

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

300

600

900

1200

1500

<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:

0.158

Hom.:

5359

Bravo

AF:

0.181

Asia WGS

AF:

0.446

AC:

1550

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

0.41

(source)

DANN

Benign

0.25

PhyloP100

-0.61

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