dbSNP rs79085477: LOC105372685:n.277+5836G>A (chr20-57126159-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_007067759.1(LOC105372685):n.277+5836G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 151,688 control chromosomes in the GnomAD database, including 70 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 0.022 ( 70 hom., cov: 31)

Consequence

LOC105372685
XR_007067759.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.466

Publications

5 publications found

Variant links:

Genes affected

LOC105372685 (HGNC:):

LOC105372685 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105372685	XR_007067759.1 link	n.277+5836G>A	intron_variant	Intron 2 of 3
LOC105372685	XR_007067760.1 link	n.270+5836G>A	intron_variant	Intron 2 of 3
LOC105372685	XR_936901.3 link	n.282+5836G>A	intron_variant	Intron 2 of 4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.0223

AC:

3376

AN:

151572

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0545

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00985

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.0525

Gnomad SAS

AF:

0.0312

Gnomad FIN

AF:

0.000478

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00745

Gnomad OTH

AF:

0.0178

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

GnomAD4 genome

AF:

0.0223

AC:

3384

AN:

151688

Hom.:

Cov.:

AF XY:

0.0216

AC XY:

1601

AN XY:

74086

show subpopulations

African (AFR)

AF:

0.0545

AC:

2252

AN:

41304

American (AMR)

AF:

0.00983

AC:

150

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.00317

AC:

AN:

3468

East Asian (EAS)

AF:

0.0528

AC:

273

AN:

5166

South Asian (SAS)

AF:

0.0310

AC:

149

AN:

4804

European-Finnish (FIN)

AF:

0.000478

AC:

AN:

10470

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00745

AC:

506

AN:

67916

Other (OTH)

AF:

0.0176

AC:

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

165

331

496

662

827

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<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:

0.0173

Hom.:

Bravo

AF:

0.0242

Asia WGS

AF:

0.0830

AC:

288

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.41

(source)

DANN

Benign

0.31

PhyloP100

-0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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