Genetic Variant LOC105369955:n.352+697A>G (chr12-105427670-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_945295.3(LOC105369955):n.352+697A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,138 control chromosomes in the GnomAD database, including 1,826 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 0.15 ( 1826 hom., cov: 32)

Consequence

LOC105369955
XR_945295.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.393

Publications

7 publications found

Variant links:

Genes affected

LOC105369955 (HGNC:):

LOC105369955 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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369955	XR_945295.3 link	n.352+697A>G		intron_variant	Intron 1 of 2
LOC105369956	XR_945297.3 link	n.495-907T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

22805

AN:

152020

Hom.:

1828

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.150

AC:

22809

AN:

152138

Hom.:

1826

Cov.:

AF XY:

0.150

AC XY:

11138

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.147

AC:

6093

AN:

41516

American (AMR)

AF:

0.160

AC:

2439

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

477

AN:

3472

East Asian (EAS)

AF:

0.000965

AC:

AN:

5184

South Asian (SAS)

AF:

0.146

AC:

706

AN:

4830

European-Finnish (FIN)

AF:

0.159

AC:

1680

AN:

10560

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10829

AN:

67984

Other (OTH)

AF:

0.161

AC:

339

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1019

2037

3056

4074

5093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

258

516

774

1032

1290

<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.:

3005

Bravo

AF:

0.150

Asia WGS

AF:

0.0710

AC:

248

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.4

(source)

DANN

Benign

0.73

PhyloP100

0.39

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