dbSNP rs17109831: LOC112268135:n.326+26818G>T (chr14-25403290-G-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_002957614.1(LOC112268135):n.326+26818G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,038 control chromosomes in the GnomAD database, including 3,268 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 0.19 ( 3268 hom., cov: 32)

Consequence

LOC112268135
XR_002957614.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.182

Publications

0 publications found

Variant links:

Genes affected

LOC112268135 (HGNC:):

LOC112268135 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268135	XR_002957614.1 link	n.326+26818G>T		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.188

AC:

28637

AN:

151922

Hom.:

3249

Cov.:

show subpopulations

Gnomad AFR

AF:

0.305

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0780

Gnomad FIN

AF:

0.197

Gnomad MID

AF:

0.0796

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.172

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

GnomAD4 genome

AF:

0.189

AC:

28701

AN:

152038

Hom.:

3268

Cov.:

AF XY:

0.186

AC XY:

13807

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.305

AC:

12652

AN:

41416

American (AMR)

AF:

0.123

AC:

1879

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

382

AN:

3472

East Asian (EAS)

AF:

0.00136

AC:

AN:

5164

South Asian (SAS)

AF:

0.0782

AC:

377

AN:

4818

European-Finnish (FIN)

AF:

0.197

AC:

2086

AN:

10592

Middle Eastern (MID)

AF:

0.0822

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.156

AC:

10616

AN:

67984

Other (OTH)

AF:

0.170

AC:

359

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1166

2332

3499

4665

5831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<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:

0.160

Hom.:

3491

Bravo

AF:

0.189

Asia WGS

AF:

0.0630

AC:

219

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.0

(source)

DANN

Benign

0.72

PhyloP100

0.18

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