dbSNP rs6733000: ENSG00000231204:n.194-70025C>T (chr2-21729332-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 ENST00000435237.1(ENSG00000231204):n.194-70025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,026 control chromosomes in the GnomAD database, including 937 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 0.10 ( 937 hom., cov: 32)

Consequence

ENSG00000231204
ENST00000435237.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00500

Publications

0 publications found

Variant links:

Genes affected

ENSG00000231204 (HGNC:):

ENSG00000231204 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 (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000231204	ENST00000435237.1 link	n.194-70025C>T	intron_variant	Intron 3 of 5	3
ENSG00000231204	ENST00000717099.1 link	n.556-70025C>T	intron_variant	Intron 5 of 6
ENSG00000231204	ENST00000753412.1 link	n.187+1743C>T	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.102

AC:

15485

AN:

151908

Hom.:

928

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0964

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.0343

Gnomad SAS

AF:

0.0559

Gnomad FIN

AF:

0.0567

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0819

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.102

AC:

15518

AN:

152026

Hom.:

937

Cov.:

AF XY:

0.0999

AC XY:

7426

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.163

AC:

6750

AN:

41484

American (AMR)

AF:

0.0961

AC:

1467

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

390

AN:

3464

East Asian (EAS)

AF:

0.0344

AC:

176

AN:

5120

South Asian (SAS)

AF:

0.0557

AC:

269

AN:

4828

European-Finnish (FIN)

AF:

0.0567

AC:

602

AN:

10610

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0819

AC:

5565

AN:

67942

Other (OTH)

AF:

0.110

AC:

233

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

706

1413

2119

2826

3532

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

168

336

504

672

840

<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:

0.0862

Hom.:

331

Bravo

AF:

0.109

Asia WGS

AF:

0.0690

AC:

241

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

2.8

(source)

DANN

Benign

0.45

PhyloP100

0.0050

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