Genetic Variant LOC105369710:n.155+16459C>A (chr12-28090647-G-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_931461.3(LOC105369710):n.155+16459C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,910 control chromosomes in the GnomAD database, including 3,940 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 0.22 ( 3940 hom., cov: 31)

Consequence

LOC105369710
XR_931461.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0940

Publications

7 publications found

Variant links:

COSMIC-nc: COSV101081868

Genes affected

LOC105369710 (HGNC:):

LOC105369710 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369710	XR_931461.3 link	n.155+16459C>A		intron_variant	Intron 2 of 2
LOC105369710	XR_931462.3 link	n.156-1792C>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32846

AN:

151792

Hom.:

3934

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.276

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.199

Gnomad OTH

AF:

0.220

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

GnomAD4 genome

AF:

0.216

AC:

32865

AN:

151910

Hom.:

3940

Cov.:

AF XY:

0.221

AC XY:

16384

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.183

AC:

7580

AN:

41442

American (AMR)

AF:

0.322

AC:

4918

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

673

AN:

3466

East Asian (EAS)

AF:

0.431

AC:

2209

AN:

5120

South Asian (SAS)

AF:

0.277

AC:

1325

AN:

4792

European-Finnish (FIN)

AF:

0.183

AC:

1943

AN:

10592

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.199

AC:

13547

AN:

67930

Other (OTH)

AF:

0.220

AC:

464

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1276

2552

3829

5105

6381

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.205

Hom.:

9736

Bravo

AF:

0.222

Asia WGS

AF:

0.318

AC:

1104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.7

(source)

DANN

Benign

0.66

PhyloP100

0.094

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