dbSNP rs12760731: LOC101928866:n.1269-546G>A (chr1-178502087-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_001738305.2(LOC101928866):n.1269-546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,244 control chromosomes in the GnomAD database, including 1,220 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 ( 1220 hom., cov: 33)

Consequence

LOC101928866
XR_001738305.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.397

Publications

6 publications found

Variant links:

Genes affected

LOC101928866 (HGNC:):

LOC101928866 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 = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928866	XR_001738305.2 link	n.1269-546G>A		intron_variant	Intron 5 of 5
LOC101928866	XR_001738307.2 link	n.955-546G>A		intron_variant	Intron 5 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17634

AN:

152126

Hom.:

1209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.0794

Gnomad ASJ

AF:

0.0559

Gnomad EAS

AF:

0.0547

Gnomad SAS

AF:

0.0507

Gnomad FIN

AF:

0.0627

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.0987

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.116

AC:

17681

AN:

152244

Hom.:

1220

Cov.:

AF XY:

0.112

AC XY:

8344

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.193

AC:

8020

AN:

41522

American (AMR)

AF:

0.0791

AC:

1211

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.0559

AC:

194

AN:

3470

East Asian (EAS)

AF:

0.0544

AC:

282

AN:

5180

South Asian (SAS)

AF:

0.0504

AC:

243

AN:

4824

European-Finnish (FIN)

AF:

0.0627

AC:

665

AN:

10608

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0987

AC:

6710

AN:

68010

Other (OTH)

AF:

0.116

AC:

245

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

797

1593

2390

3186

3983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<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:

0.107

Hom.:

627

Bravo

AF:

0.119

Asia WGS

AF:

0.117

AC:

405

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

1.8

(source)

DANN

Benign

0.59

PhyloP100

-0.40

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