dbSNP rs2016167: ENSG00000305424:n.794+237G>T (chr5-113714894-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000810863.1(ENSG00000305424):n.794+237G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,178 control chromosomes in the GnomAD database, including 3,663 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 0.20 ( 3663 hom., cov: 33)

Consequence

ENSG00000305424
ENST00000810863.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.52

Publications

1 publications found

Variant links:

Genes affected

ENSG00000305424 (HGNC:):

ENSG00000305424 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 = 0.325 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
ENSG00000305424	ENST00000810863.1 link	n.794+237G>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30934

AN:

152060

Hom.:

3662

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.0231

Gnomad SAS

AF:

0.0930

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.171

Gnomad OTH

AF:

0.174

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

GnomAD4 genome

AF:

0.203

AC:

30964

AN:

152178

Hom.:

3663

Cov.:

AF XY:

0.197

AC XY:

14653

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.329

AC:

13670

AN:

41492

American (AMR)

AF:

0.171

AC:

2620

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

411

AN:

3472

East Asian (EAS)

AF:

0.0231

AC:

120

AN:

5188

South Asian (SAS)

AF:

0.0930

AC:

449

AN:

4826

European-Finnish (FIN)

AF:

0.148

AC:

1569

AN:

10590

Middle Eastern (MID)

AF:

0.0816

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.171

AC:

11596

AN:

68006

Other (OTH)

AF:

0.173

AC:

366

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1242

2485

3727

4970

6212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.200

Hom.:

428

Bravo

AF:

0.209

Asia WGS

AF:

0.0630

AC:

219

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

0.90

(source)

DANN

Benign

0.17

PhyloP100

-2.5

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