Genetic Variant ENSG00000300871:n.248+5338A>G (chr11-93613320-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000774790.1(ENSG00000300871):n.248+5338A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,022 control chromosomes in the GnomAD database, including 15,194 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 0.44 ( 15194 hom., cov: 32)

Consequence

ENSG00000300871
ENST00000774790.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.273

Publications

5 publications found

Variant links:

Genes affected

ENSG00000300871 (HGNC:):

ENSG00000300871 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=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300871	ENST00000774790.1 link	n.248+5338A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66700

AN:

151904

Hom.:

15182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.622

Gnomad AMR

AF:

0.571

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.506

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.464

Gnomad OTH

AF:

0.430

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

GnomAD4 genome

AF:

0.439

AC:

66729

AN:

152022

Hom.:

15194

Cov.:

AF XY:

0.440

AC XY:

32730

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.332

AC:

13748

AN:

41472

American (AMR)

AF:

0.572

AC:

8723

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.520

AC:

1804

AN:

3470

East Asian (EAS)

AF:

0.475

AC:

2456

AN:

5170

South Asian (SAS)

AF:

0.507

AC:

2443

AN:

4822

European-Finnish (FIN)

AF:

0.419

AC:

4426

AN:

10572

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.464

AC:

31539

AN:

67946

Other (OTH)

AF:

0.425

AC:

896

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1856

3712

5569

7425

9281

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

622

1244

1866

2488

3110

<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:

0.464

Hom.:

26979

Bravo

AF:

0.446

Asia WGS

AF:

0.453

AC:

1577

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.8

(source)

DANN

Benign

0.79

PhyloP100

0.27

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