Genetic Variant XR_943790.3:n.829+10096T>G (chr14-40602267-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_943790.3(LOC105370466):n.829+10096T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 152,000 control chromosomes in the GnomAD database, including 18,357 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 0.48 ( 18357 hom., cov: 33)

Consequence

LOC105370466
XR_943790.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.399

Publications

2 publications found

Variant links:

Genes affected

LOC105370466 (HGNC:):

LOC105370466 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370466	XR_943790.3 link	n.829+10096T>G		intron_variant	Intron 2 of 2
LOC105370466	XR_943792.3 link	n.840-9105T>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72335

AN:

151880

Hom.:

18335

Cov.:

show subpopulations

Gnomad AFR

AF:

0.661

Gnomad AMI

AF:

0.456

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.451

Gnomad EAS

AF:

0.538

Gnomad SAS

AF:

0.513

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.375

Gnomad OTH

AF:

0.453

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

GnomAD4 genome

AF:

0.476

AC:

72413

AN:

152000

Hom.:

18357

Cov.:

AF XY:

0.480

AC XY:

35653

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.661

AC:

27432

AN:

41470

American (AMR)

AF:

0.460

AC:

7019

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.451

AC:

1565

AN:

3468

East Asian (EAS)

AF:

0.538

AC:

2781

AN:

5166

South Asian (SAS)

AF:

0.512

AC:

2472

AN:

4826

European-Finnish (FIN)

AF:

0.390

AC:

4120

AN:

10560

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.376

AC:

25513

AN:

67944

Other (OTH)

AF:

0.454

AC:

957

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1845

3689

5534

7378

9223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

646

1292

1938

2584

3230

<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:

0.433

Hom.:

1993

Bravo

AF:

0.490

Asia WGS

AF:

0.533

AC:

1854

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.4

(source)

DANN

Benign

0.90

PhyloP100

-0.40

Splicing

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

Publications

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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