Genetic Variant ENST00000722344.1:n.77-83G>A (chr16-27378090-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000722344.1(ENSG00000294275):n.77-83G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,058 control chromosomes in the GnomAD database, including 8,895 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 0.32 ( 8895 hom., cov: 32)

Consequence

ENSG00000294275
ENST00000722344.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.286

Publications

9 publications found

Variant links:

Genes affected

ENSG00000294275 (HGNC:):

ENSG00000294275 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000294275	ENST00000722344.1 link	n.77-83G>A	intron_variant	Intron 1 of 1
ENSG00000294275	ENST00000722345.1 link	n.173+28G>A	intron_variant	Intron 2 of 2
ENSG00000294275	ENST00000722346.1 link	n.28-83G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48070

AN:

151940

Hom.:

8874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.286

Gnomad AMR

AF:

0.234

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.282

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.287

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

GnomAD4 genome

AF:

0.317

AC:

48131

AN:

152058

Hom.:

8895

Cov.:

AF XY:

0.312

AC XY:

23214

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.518

AC:

21490

AN:

41448

American (AMR)

AF:

0.234

AC:

3571

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

937

AN:

3466

East Asian (EAS)

AF:

0.200

AC:

1035

AN:

5176

South Asian (SAS)

AF:

0.130

AC:

627

AN:

4826

European-Finnish (FIN)

AF:

0.282

AC:

2979

AN:

10578

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.244

AC:

16552

AN:

67960

Other (OTH)

AF:

0.286

AC:

604

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1537

3074

4610

6147

7684

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<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:

0.260

Hom.:

26349

Bravo

AF:

0.323

Asia WGS

AF:

0.184

AC:

637

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.78

(source)

DANN

Benign

0.62

PhyloP100

0.29

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