Genetic Variant ENSG00000305956:n.273-1123G>A (chr7-52842345-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 ENST00000814334.1(ENSG00000305956):n.273-1123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,754 control chromosomes in the GnomAD database, including 8,342 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 ( 8342 hom., cov: 32)

Consequence

ENSG00000305956
ENST00000814334.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660

Publications

3 publications found

Variant links:

Genes affected

ENSG00000305956 (HGNC:):

ENSG00000305956 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901805	XR_007060629.1 link	n.78-1123G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305956	ENST00000814334.1 link	n.273-1123G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.330

AC:

49984

AN:

151636

Hom.:

8329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.204

Gnomad AMR

AF:

0.293

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.330

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.334

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

GnomAD4 genome

AF:

0.330

AC:

50051

AN:

151754

Hom.:

8342

Cov.:

AF XY:

0.333

AC XY:

24674

AN XY:

74134

show subpopulations

African (AFR)

AF:

0.376

AC:

15537

AN:

41374

American (AMR)

AF:

0.293

AC:

4460

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

1143

AN:

3468

East Asian (EAS)

AF:

0.251

AC:

1285

AN:

5128

South Asian (SAS)

AF:

0.455

AC:

2177

AN:

4788

European-Finnish (FIN)

AF:

0.343

AC:

3609

AN:

10534

Middle Eastern (MID)

AF:

0.331

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.307

AC:

20856

AN:

67910

Other (OTH)

AF:

0.332

AC:

702

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.526

Heterozygous variant carriers

1698

3396

5093

6791

8489

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

506

1012

1518

2024

2530

<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:

0.319

Hom.:

1340

Bravo

AF:

0.324

Asia WGS

AF:

0.372

AC:

1294

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.45

(source)

DANN

Benign

0.47

PhyloP100

-0.066

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