Genetic Variant LOC124902741:n.1992-2766T>C (chr11-102862432-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_007062868.1(LOC124902741):n.1992-2766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,246 control chromosomes in the GnomAD database, including 1,288 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 0.12 ( 1288 hom., cov: 32)

Consequence

LOC124902741
XR_007062868.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.157

Publications

26 publications found

Variant links:

Genes affected

LOC124902741 (HGNC:):

LOC124902741 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902741	XR_007062868.1 link	n.1992-2766T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18275

AN:

152128

Hom.:

1289

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0587

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.0674

Gnomad SAS

AF:

0.0993

Gnomad FIN

AF:

0.177

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.138

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

GnomAD4 genome

AF:

0.120

AC:

18263

AN:

152246

Hom.:

1288

Cov.:

AF XY:

0.120

AC XY:

8924

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0585

AC:

2432

AN:

41560

American (AMR)

AF:

0.109

AC:

1671

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.186

AC:

647

AN:

3472

East Asian (EAS)

AF:

0.0670

AC:

347

AN:

5178

South Asian (SAS)

AF:

0.0987

AC:

476

AN:

4822

European-Finnish (FIN)

AF:

0.177

AC:

1876

AN:

10602

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.152

AC:

10328

AN:

67998

Other (OTH)

AF:

0.136

AC:

287

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

813

1627

2440

3254

4067

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

194

388

582

776

970

<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:

0.139

Hom.:

1479

Bravo

AF:

0.111

Asia WGS

AF:

0.0830

AC:

290

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.7

(source)

DANN

Benign

0.36

PhyloP100

0.16

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