Genetic Variant LOC107984390:n.5178+9945G>T (chr11-113671388-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001748390.2(LOC107984390):n.5178+9945G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 152,148 control chromosomes in the GnomAD database, including 645 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 0.081 ( 645 hom., cov: 32)

Consequence

LOC107984390
XR_001748390.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

1 publications found

Variant links:

Genes affected

LOC107984390 (HGNC:):

LOC107984390 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=-0.94).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984390	XR_001748390.2 link	n.5178+9945G>T		intron_variant	Intron 1 of 2
LOC107984390	XR_001748391.2 link	n.5178+9945G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.0808

AC:

12278

AN:

152030

Hom.:

644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0229

Gnomad AMI

AF:

0.137

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.0433

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0673

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0726

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

GnomAD4 genome

AF:

0.0807

AC:

12277

AN:

152148

Hom.:

645

Cov.:

AF XY:

0.0791

AC XY:

5882

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.0228

AC:

947

AN:

41524

American (AMR)

AF:

0.0998

AC:

1525

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0433

AC:

150

AN:

3468

East Asian (EAS)

AF:

0.00135

AC:

AN:

5178

South Asian (SAS)

AF:

0.0676

AC:

326

AN:

4824

European-Finnish (FIN)

AF:

0.105

AC:

1110

AN:

10580

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.117

AC:

7927

AN:

67984

Other (OTH)

AF:

0.0714

AC:

151

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

569

1139

1708

2278

2847

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.0926

Hom.:

102

Bravo

AF:

0.0753

Asia WGS

AF:

0.0360

AC:

126

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.18

(source)

DANN

Benign

0.50

PhyloP100

-1.4

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