Genetic Variant LOC105376584:n.87-2925T>A (chr11-20564617-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_931105.1(LOC105376584):n.87-2925T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,118 control chromosomes in the GnomAD database, including 3,863 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 0.18 ( 3863 hom., cov: 32)

Consequence

LOC105376584
XR_931105.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Publications

3 publications found

Variant links:

Genes affected

LOC105376584 (HGNC:):

LOC105376584 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376584	XR_931105.1 link	n.87-2925T>A		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26768

AN:

152000

Hom.:

3837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.378

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.331

Gnomad SAS

AF:

0.0613

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0680

Gnomad OTH

AF:

0.151

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

GnomAD4 genome

AF:

0.176

AC:

26847

AN:

152118

Hom.:

3863

Cov.:

AF XY:

0.175

AC XY:

12997

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.378

AC:

15667

AN:

41424

American (AMR)

AF:

0.180

AC:

2755

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.166

AC:

576

AN:

3470

East Asian (EAS)

AF:

0.332

AC:

1719

AN:

5180

South Asian (SAS)

AF:

0.0615

AC:

297

AN:

4826

European-Finnish (FIN)

AF:

0.0802

AC:

850

AN:

10602

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0680

AC:

4628

AN:

68014

Other (OTH)

AF:

0.149

AC:

315

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

984

1968

2953

3937

4921

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.125

Hom.:

277

Bravo

AF:

0.198

Asia WGS

AF:

0.199

AC:

695

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

3.2

(source)

DANN

Benign

0.75

PhyloP100

-0.17

Splicing

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

Publications

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11-20564617-A-T

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