dbSNP rs4672503: ENSG00000228541:n.199+25703C>T (chr2-62322149-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 ENST00000687402.3(ENSG00000228541):n.199+25703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,034 control chromosomes in the GnomAD database, including 8,577 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 0.33 ( 8577 hom., cov: 32)

Consequence

ENSG00000228541
ENST00000687402.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

Publications

7 publications found

Variant links:

Genes affected

ENSG00000228541 (HGNC:):

ENSG00000228541 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=-0.75).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000228541	ENST00000687402.3 link	n.199+25703C>T	intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2 link	n.199+25703C>T	intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000688476.3 link	n.202-23765C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49428

AN:

151916

Hom.:

8584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.341

Gnomad EAS

AF:

0.429

Gnomad SAS

AF:

0.273

Gnomad FIN

AF:

0.234

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.329

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

GnomAD4 genome

AF:

0.325

AC:

49432

AN:

152034

Hom.:

8577

Cov.:

AF XY:

0.320

AC XY:

23811

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.435

AC:

18007

AN:

41430

American (AMR)

AF:

0.304

AC:

4651

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

1185

AN:

3470

East Asian (EAS)

AF:

0.429

AC:

2218

AN:

5176

South Asian (SAS)

AF:

0.271

AC:

1307

AN:

4818

European-Finnish (FIN)

AF:

0.234

AC:

2468

AN:

10550

Middle Eastern (MID)

AF:

0.422

AC:

124

AN:

294

European-Non Finnish (NFE)

AF:

0.273

AC:

18574

AN:

67984

Other (OTH)

AF:

0.326

AC:

689

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1650

3301

4951

6602

8252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.295

Hom.:

11617

Bravo

AF:

0.340

Asia WGS

AF:

0.348

AC:

1207

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

8.1

(source)

DANN

Benign

0.83

PhyloP100

-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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