Genetic Variant ENSG00000272744:n.*43G>T (chr4-183517570-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000608204.1(ENSG00000272744):n.*43G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,678 control chromosomes in the GnomAD database, including 5,170 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 0.26 ( 5167 hom., cov: 31)

Exomes 𝑓: 0.19 ( 3 hom. )

Consequence

ENSG00000272744
ENST00000608204.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.26

Publications

3 publications found

Variant links:

COSMIC-nc: COSV74179756

Genes affected

ENSG00000272744 (HGNC:):

ENSG00000272744 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=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000608204.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272744	ENST00000608204.1	TSL:6	n.*43G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38625

AN:

151314

Hom.:

5173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.444

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.187

AC:

AN:

246

Hom.:

Cov.:

AF XY:

0.176

AC XY:

AN XY:

188

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.438

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.161

AC:

AN:

180

Other (OTH)

AF:

0.182

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.255

AC:

38628

AN:

151432

Hom.:

5167

Cov.:

AF XY:

0.260

AC XY:

19252

AN XY:

73940

show subpopulations

African (AFR)

AF:

0.283

AC:

11675

AN:

41252

American (AMR)

AF:

0.216

AC:

3280

AN:

15184

Ashkenazi Jewish (ASJ)

AF:

0.346

AC:

1198

AN:

3460

East Asian (EAS)

AF:

0.443

AC:

2283

AN:

5148

South Asian (SAS)

AF:

0.237

AC:

1140

AN:

4800

European-Finnish (FIN)

AF:

0.303

AC:

3177

AN:

10482

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.219

AC:

14822

AN:

67808

Other (OTH)

AF:

0.268

AC:

562

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1410

2821

4231

5642

7052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.226

Hom.:

1849

Bravo

AF:

0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

(source)

DANN

Benign

0.49

PhyloP100

-2.3

Mutation Taster

=100/0

polymorphism

(source)

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