dbSNP rs1981105: ENSG00000293214:n.88-3619C>T (chr20-4633840-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000652447.1(ENSG00000293214):n.88-3619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,096 control chromosomes in the GnomAD database, including 3,817 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 0.22 ( 3817 hom., cov: 32)

Consequence

ENSG00000293214
ENST00000652447.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.727

Publications

2 publications found

Variant links:

Genes affected

ENSG00000293214 (HGNC:):

ENSG00000293214 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 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
ENSG00000293214	ENST00000652447.1 link	n.88-3619C>T		intron_variant	Intron 1 of 1
ENSG00000293214	ENST00000773443.1 link	n.132-3619C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32881

AN:

151978

Hom.:

3816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.0724

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.392

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.199

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

GnomAD4 genome

AF:

0.216

AC:

32900

AN:

152096

Hom.:

3817

Cov.:

AF XY:

0.222

AC XY:

16488

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.158

AC:

6548

AN:

41508

American (AMR)

AF:

0.283

AC:

4331

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.184

AC:

638

AN:

3472

East Asian (EAS)

AF:

0.392

AC:

2031

AN:

5176

South Asian (SAS)

AF:

0.253

AC:

1217

AN:

4812

European-Finnish (FIN)

AF:

0.274

AC:

2894

AN:

10552

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.216

AC:

14713

AN:

67962

Other (OTH)

AF:

0.197

AC:

417

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1326

2652

3977

5303

6629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

342

684

1026

1368

1710

<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:

0.214

Hom.:

2204

Bravo

AF:

0.214

Asia WGS

AF:

0.348

AC:

1211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.7

(source)

DANN

Benign

0.82

PhyloP100

-0.73

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