Genetic Variant XR_947985.1: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:

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=-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

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

XR_947985.1:n.102-16025C>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