Genetic Variant XR_001746599.1:n.142+81031T>C (chr9-1799943-T-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_001746599.1(LOC105375951):n.142+81031T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,258 control chromosomes in the GnomAD database, including 1,085 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 0.11 ( 1085 hom., cov: 32)

Consequence

LOC105375951
XR_001746599.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Publications

1 publications found

Variant links:

Genes affected

LOC105375951 (HGNC:):

LOC105375951 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375951	XR_001746599.1 link	n.142+81031T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.112

AC:

17100

AN:

152140

Hom.:

1080

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.0764

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.0930

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.102

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

GnomAD4 genome

AF:

0.113

AC:

17133

AN:

152258

Hom.:

1085

Cov.:

AF XY:

0.114

AC XY:

8519

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.111

AC:

4615

AN:

41544

American (AMR)

AF:

0.0763

AC:

1167

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

380

AN:

3468

East Asian (EAS)

AF:

0.0933

AC:

484

AN:

5190

South Asian (SAS)

AF:

0.125

AC:

605

AN:

4830

European-Finnish (FIN)

AF:

0.152

AC:

1607

AN:

10606

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.112

AC:

7631

AN:

68004

Other (OTH)

AF:

0.101

AC:

214

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

783

1565

2348

3130

3913

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.110

Hom.:

1563

Bravo

AF:

0.108

Asia WGS

AF:

0.118

AC:

411

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.3

(source)

DANN

Benign

0.55

PhyloP100

-0.17

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