dbSNP rs1562900: ENSG00000231204:n.194-75790T>C (chr2-21723567-T-C) – 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.194-75790T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,028 control chromosomes in the GnomAD database, including 2,179 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 0.15 ( 2179 hom., cov: 32)

Consequence

ENSG00000231204
ENST00000435237.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.75

Publications

1 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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.194-75790T>C	intron_variant	Intron 3 of 5	3
ENSG00000231204	ENST00000717099.1 link	n.556-75790T>C	intron_variant	Intron 5 of 6
ENSG00000231204	ENST00000753412.1 link	n.74-3827T>C	intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.147

AC:

22379

AN:

151910

Hom.:

2160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.271

Gnomad AMI

AF:

0.0527

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0659

Gnomad SAS

AF:

0.0960

Gnomad FIN

AF:

0.0670

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.155

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

GnomAD4 genome

AF:

0.148

AC:

22435

AN:

152028

Hom.:

2179

Cov.:

AF XY:

0.145

AC XY:

10752

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.272

AC:

11291

AN:

41464

American (AMR)

AF:

0.123

AC:

1871

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

458

AN:

3468

East Asian (EAS)

AF:

0.0658

AC:

338

AN:

5136

South Asian (SAS)

AF:

0.0955

AC:

460

AN:

4818

European-Finnish (FIN)

AF:

0.0670

AC:

710

AN:

10598

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.101

AC:

6887

AN:

67968

Other (OTH)

AF:

0.155

AC:

327

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

926

1852

2777

3703

4629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.113

Hom.:

580

Bravo

AF:

0.158

Asia WGS

AF:

0.115

AC:

399

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.082

(source)

DANN

Benign

0.59

PhyloP100

-2.8

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