Genetic Variant ENSG00000229618:n.237-25661T>G (chr7-13284548-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000411542.1(ENSG00000229618):n.237-25661T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 152,294 control chromosomes in the GnomAD database, including 157 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 0.024 ( 157 hom., cov: 32)

Consequence

ENSG00000229618
ENST00000411542.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.142

Publications

0 publications found

Variant links:

Genes affected

ENSG00000229618 (HGNC:):

ENSG00000229618 links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 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
ENSG00000229618	ENST00000411542.1 link	n.237-25661T>G	intron_variant	Intron 2 of 4	4
ENSG00000229618	ENST00000638964.1 link	n.609-25661T>G	intron_variant	Intron 2 of 5	5
ENSG00000229618	ENST00000639998.1 link	n.608-25661T>G	intron_variant	Intron 4 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.0239

AC:

3631

AN:

152176

Hom.:

161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00449

Gnomad AMI

AF:

0.0976

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.0944

Gnomad FIN

AF:

0.00668

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0182

Gnomad OTH

AF:

0.0301

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

GnomAD4 genome

AF:

0.0237

AC:

3616

AN:

152294

Hom.:

157

Cov.:

AF XY:

0.0255

AC XY:

1896

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.00447

AC:

186

AN:

41574

American (AMR)

AF:

0.0244

AC:

373

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0231

AC:

AN:

3470

East Asian (EAS)

AF:

0.204

AC:

1057

AN:

5174

South Asian (SAS)

AF:

0.0935

AC:

451

AN:

4826

European-Finnish (FIN)

AF:

0.00668

AC:

AN:

10624

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0182

AC:

1238

AN:

68000

Other (OTH)

AF:

0.0307

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

180

359

539

718

898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

150

200

250

<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:

0.0172

Hom.:

Bravo

AF:

0.0241

Asia WGS

AF:

0.145

AC:

503

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.1

(source)

DANN

Benign

0.57

PhyloP100

0.14

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