Genetic Variant ENSG00000297869:n.192+39111A>G (chr11-114833570-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 ENST00000751459.1(ENSG00000297869):n.192+39111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,932 control chromosomes in the GnomAD database, including 9,131 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 0.34 ( 9131 hom., cov: 32)

Consequence

ENSG00000297869
ENST00000751459.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0370

Publications

1 publications found

Variant links:

Genes affected

ENSG00000297869 (HGNC:):

ENSG00000297869 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369506	XR_948042.3 link	n.86+39111A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297869	ENST00000751459.1 link	n.192+39111A>G		intron_variant	Intron 2 of 3
ENSG00000297869	ENST00000751460.1 link	n.214+39111A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51702

AN:

151814

Hom.:

9123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.406

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.572

Gnomad SAS

AF:

0.417

Gnomad FIN

AF:

0.304

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.315

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

GnomAD4 genome

AF:

0.340

AC:

51732

AN:

151932

Hom.:

9131

Cov.:

AF XY:

0.347

AC XY:

25787

AN XY:

74256

show subpopulations

African (AFR)

AF:

0.342

AC:

14149

AN:

41402

American (AMR)

AF:

0.406

AC:

6203

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.332

AC:

1154

AN:

3472

East Asian (EAS)

AF:

0.573

AC:

2948

AN:

5146

South Asian (SAS)

AF:

0.417

AC:

2007

AN:

4818

European-Finnish (FIN)

AF:

0.304

AC:

3208

AN:

10564

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.309

AC:

20994

AN:

67942

Other (OTH)

AF:

0.320

AC:

674

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1713

3425

5138

6850

8563

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

522

1044

1566

2088

2610

<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:

0.322

Hom.:

1637

Bravo

AF:

0.343

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.0

(source)

DANN

Benign

0.85

PhyloP100

-0.037

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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