dbSNP rs201647: LOC107985709:n.858+312G>A (chrX-127248230-C-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_001755952.1(LOC107985709):n.858+312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0303 in 111,594 control chromosomes in the GnomAD database, including 92 homozygotes. There are 973 hemizygotes in GnomAD. 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 0.030 ( 92 hom., 973 hem., cov: 23)

Consequence

LOC107985709
XR_001755952.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.77

Publications

2 publications found

Variant links:

Genes affected

LOC107985709 (HGNC:):

LOC107985709 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.086 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107985709	XR_001755952.1 link	n.858+312G>A	intron_variant	Intron 6 of 6
LOC107985709	XR_001755954.1 link	n.220+312G>A	intron_variant	Intron 3 of 3
LOC107985709	XR_001755955.1 link	n.866+304G>A	intron_variant	Intron 6 of 6

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0302

AC:

3367

AN:

111542

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0885

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.0212

Gnomad EAS

AF:

0.00197

Gnomad SAS

AF:

0.0442

Gnomad FIN

AF:

0.000167

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00311

Gnomad OTH

AF:

0.0341

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

GnomAD4 genome

AF:

0.0303

AC:

3378

AN:

111594

Hom.:

Cov.:

AF XY:

0.0288

AC XY:

973

AN XY:

33810

show subpopulations

African (AFR)

AF:

0.0888

AC:

2727

AN:

30708

American (AMR)

AF:

0.0233

AC:

244

AN:

10476

Ashkenazi Jewish (ASJ)

AF:

0.0212

AC:

AN:

2643

East Asian (EAS)

AF:

0.00197

AC:

AN:

3549

South Asian (SAS)

AF:

0.0440

AC:

119

AN:

2702

European-Finnish (FIN)

AF:

0.000167

AC:

AN:

5986

Middle Eastern (MID)

AF:

0.0276

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.00309

AC:

164

AN:

53118

Other (OTH)

AF:

0.0337

AC:

AN:

1513

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

124

248

372

496

620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<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:

0.0209

Hom.:

Bravo

AF:

0.0369

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.047

(source)

DANN

Benign

0.19

PhyloP100

-1.8

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