Genetic Variant ENST00000757672.1:n.224-20548G>T (chr7-85987149-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000757672.1(ENSG00000298738):n.224-20548G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,044 control chromosomes in the GnomAD database, including 2,678 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 0.17 ( 2678 hom., cov: 32)

Consequence

ENSG00000298738
ENST00000757672.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92

Publications

3 publications found

Variant links:

Genes affected

ENSG00000298738 (HGNC:):

ENSG00000298738 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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757672.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298738	ENST00000757672.1		n.224-20548G>T		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25945

AN:

151926

Hom.:

2677

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0533

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.163

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.176

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.194

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

GnomAD4 genome

AF:

0.171

AC:

25940

AN:

152044

Hom.:

2678

Cov.:

AF XY:

0.171

AC XY:

12681

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0532

AC:

2209

AN:

41530

American (AMR)

AF:

0.163

AC:

2481

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

866

AN:

3464

East Asian (EAS)

AF:

0.177

AC:

913

AN:

5166

South Asian (SAS)

AF:

0.176

AC:

847

AN:

4818

European-Finnish (FIN)

AF:

0.222

AC:

2351

AN:

10570

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.229

AC:

15578

AN:

67944

Other (OTH)

AF:

0.193

AC:

407

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1087

2175

3262

4350

5437

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.203

Hom.:

2711

Bravo

AF:

0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.0030

(source)

DANN

Benign

0.54

PhyloP100

-1.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over