dbSNP rs1039189: ENSG00000293986:n.74+3715A>C (chr18-53951084-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000720335.1(ENSG00000293986):n.74+3715A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,078 control chromosomes in the GnomAD database, including 2,647 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 0.18 ( 2647 hom., cov: 32)

Consequence

ENSG00000293986
ENST00000720335.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.599

Publications

0 publications found

Variant links:

Genes affected

ENSG00000293986 (HGNC:):

ENSG00000293986 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 (NFE) allele frequency at 95% confidence interval = 0.232 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
ENSG00000293986	ENST00000720335.1 link	n.74+3715A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26802

AN:

151958

Hom.:

2647

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0966

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0498

Gnomad SAS

AF:

0.153

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.226

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.176

AC:

26803

AN:

152078

Hom.:

2647

Cov.:

AF XY:

0.175

AC XY:

13030

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.0966

AC:

4014

AN:

41534

American (AMR)

AF:

0.132

AC:

2019

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

573

AN:

3466

East Asian (EAS)

AF:

0.0499

AC:

259

AN:

5186

South Asian (SAS)

AF:

0.154

AC:

740

AN:

4812

European-Finnish (FIN)

AF:

0.235

AC:

2482

AN:

10572

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

15955

AN:

67920

Other (OTH)

AF:

0.164

AC:

347

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1116

2233

3349

4466

5582

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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.:

388

Bravo

AF:

0.166

Asia WGS

AF:

0.117

AC:

407

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.7

(source)

DANN

Benign

0.55

PhyloP100

0.60

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