Genetic Variant LOC124905213:n.1760A>C (chrX-129125504-T-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The XR_007068316.1(LOC124905213):n.1760A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.68 ( 18015 hom., 21775 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

LOC124905213
XR_007068316.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.454

Publications

1 publications found

Variant links:

Genes affected

LOC124905213 (HGNC:):

LOC124905213 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653849.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000225689	ENST00000653849.1	n.1101-3311A>C	intron	N/A
ENSG00000225689	ENST00000660383.1	n.144+2760A>C	intron	N/A
ENSG00000301792	ENST00000781917.1	n.49-24635T>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.675

AC:

74415

AN:

110170

Hom.:

18005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.817

Gnomad AMR

AF:

0.774

Gnomad ASJ

AF:

0.677

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.760

Gnomad FIN

AF:

0.622

Gnomad MID

AF:

0.733

Gnomad NFE

AF:

0.705

Gnomad OTH

AF:

0.713

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.676

AC:

74463

AN:

110226

Hom.:

18015

Cov.:

AF XY:

0.670

AC XY:

21775

AN XY:

32490

show subpopulations

African (AFR)

AF:

0.597

AC:

18060

AN:

30268

American (AMR)

AF:

0.775

AC:

7983

AN:

10307

Ashkenazi Jewish (ASJ)

AF:

0.677

AC:

1779

AN:

2626

East Asian (EAS)

AF:

0.600

AC:

2086

AN:

3476

South Asian (SAS)

AF:

0.763

AC:

1973

AN:

2585

European-Finnish (FIN)

AF:

0.622

AC:

3634

AN:

5839

Middle Eastern (MID)

AF:

0.744

AC:

157

AN:

211

European-Non Finnish (NFE)

AF:

0.705

AC:

37161

AN:

52735

Other (OTH)

AF:

0.717

AC:

1076

AN:

1501

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

869

1738

2606

3475

4344

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

648

1296

1944

2592

3240

<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:

0.701

Hom.:

40440

Bravo

AF:

0.686

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

2.8

(source)

DANN

Benign

0.82

PhyloP100

0.45

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over