dbSNP rs11907114: LOC105372678:n.130-815G>A (chr20-55853891-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_001754723.1(LOC105372678):n.130-815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,966 control chromosomes in the GnomAD database, including 8,696 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 0.33 ( 8696 hom., cov: 32)

Consequence

LOC105372678
XR_001754723.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670

Publications

5 publications found

Variant links:

Genes affected

LOC105372678 (HGNC:):

LOC105372678 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372678	XR_001754723.1 link	n.130-815G>A		intron_variant	Intron 1 of 2
LOC105372678	XR_001754724.1 link	n.130-815G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

50374

AN:

151848

Hom.:

8695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.113

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.335

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

GnomAD4 genome

AF:

0.332

AC:

50399

AN:

151966

Hom.:

8696

Cov.:

AF XY:

0.332

AC XY:

24677

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.388

AC:

16090

AN:

41424

American (AMR)

AF:

0.254

AC:

3875

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.435

AC:

1509

AN:

3470

East Asian (EAS)

AF:

0.114

AC:

588

AN:

5180

South Asian (SAS)

AF:

0.274

AC:

1318

AN:

4816

European-Finnish (FIN)

AF:

0.343

AC:

3617

AN:

10552

Middle Eastern (MID)

AF:

0.469

AC:

137

AN:

292

European-Non Finnish (NFE)

AF:

0.328

AC:

22264

AN:

67946

Other (OTH)

AF:

0.338

AC:

713

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1724

3448

5171

6895

8619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.330

Hom.:

25600

Bravo

AF:

0.325

Asia WGS

AF:

0.227

AC:

785

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.14

(source)

DANN

Benign

0.33

PhyloP100

-0.67

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