Genetic Variant LOC105369474:n.102-16025C>G (chr11-106393118-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_947985.1(LOC105369474):n.102-16025C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,038 control chromosomes in the GnomAD database, including 37,004 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 0.69 ( 37004 hom., cov: 31)

Consequence

LOC105369474
XR_947985.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.505

Publications

1 publications found

Variant links:

Genes affected

LOC105369474 (HGNC:):

LOC105369474 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=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369474	XR_947985.1 link	n.102-16025C>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.695

AC:

105546

AN:

151920

Hom.:

36980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.799

Gnomad AMI

AF:

0.696

Gnomad AMR

AF:

0.575

Gnomad ASJ

AF:

0.588

Gnomad EAS

AF:

0.641

Gnomad SAS

AF:

0.650

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.672

Gnomad OTH

AF:

0.662

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

GnomAD4 genome

AF:

0.695

AC:

105609

AN:

152038

Hom.:

37004

Cov.:

AF XY:

0.693

AC XY:

51490

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.799

AC:

33143

AN:

41490

American (AMR)

AF:

0.574

AC:

8770

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.588

AC:

2037

AN:

3466

East Asian (EAS)

AF:

0.641

AC:

3303

AN:

5154

South Asian (SAS)

AF:

0.649

AC:

3131

AN:

4824

European-Finnish (FIN)

AF:

0.693

AC:

7317

AN:

10564

Middle Eastern (MID)

AF:

0.701

AC:

206

AN:

294

European-Non Finnish (NFE)

AF:

0.672

AC:

45687

AN:

67962

Other (OTH)

AF:

0.656

AC:

1384

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1643

3287

4930

6574

8217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.688

Hom.:

4496

Bravo

AF:

0.686

Asia WGS

AF:

0.620

AC:

2156

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.3

(source)

DANN

Benign

0.42

PhyloP100

-0.51

Splicing

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

Publications

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11-106393118-C-G

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