dbSNP rs6065259: LOC102724968:n.243+2249C>T (chr20-40633339-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001754596.2(LOC102724968):n.243+2249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,108 control chromosomes in the GnomAD database, including 11,046 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 0.38 ( 11046 hom., cov: 33)

Consequence

LOC102724968
XR_001754596.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.115

Publications

10 publications found

Variant links:

Genes affected

LOC102724968 (HGNC:):

LOC102724968 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724968	XR_001754596.2 link	n.243+2249C>T		intron_variant	Intron 3 of 7
LOC102724968	XR_001754597.1 link	n.180+10572C>T		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57468

AN:

151990

Hom.:

11055

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.490

Gnomad EAS

AF:

0.419

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.369

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

GnomAD4 genome

AF:

0.378

AC:

57467

AN:

152108

Hom.:

11046

Cov.:

AF XY:

0.381

AC XY:

28312

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.292

AC:

12103

AN:

41500

American (AMR)

AF:

0.397

AC:

6063

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.490

AC:

1699

AN:

3470

East Asian (EAS)

AF:

0.418

AC:

2150

AN:

5148

South Asian (SAS)

AF:

0.378

AC:

1826

AN:

4826

European-Finnish (FIN)

AF:

0.436

AC:

4612

AN:

10576

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.410

AC:

27865

AN:

67982

Other (OTH)

AF:

0.365

AC:

771

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1854

3708

5561

7415

9269

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<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:

0.398

Hom.:

6350

Bravo

AF:

0.372

Asia WGS

AF:

0.350

AC:

1217

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.3

(source)

DANN

Benign

0.70

PhyloP100

-0.12

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