Genetic Variant LOC107986284:n.204+14445A>G (chr4-64789270-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_001741711.2(LOC107986284):n.204+14445A>G variant causes a intron change. The variant allele was found at a frequency of 0.218 in 152,004 control chromosomes in the GnomAD database, including 4,082 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 ( 4082 hom., cov: 32)

Consequence

LOC107986284
XR_001741711.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.02

Publications

2 publications found

Variant links:

Genes affected

LOC107986284 (HGNC:):

LOC107986284 links:

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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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986284	XR_001741711.2 link	n.204+14445A>G		intron_variant	Intron 1 of 2
LOC107986284	XR_001741712.2 link	n.383+13226A>G		intron_variant	Intron 2 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.218

AC:

33141

AN:

151886

Hom.:

4088

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.322

Gnomad ASJ

AF:

0.288

Gnomad EAS

AF:

0.459

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.215

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.260

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

GnomAD4 genome

AF:

0.218

AC:

33138

AN:

152004

Hom.:

4082

Cov.:

AF XY:

0.223

AC XY:

16537

AN XY:

74296

show subpopulations

African (AFR)

AF:

0.125

AC:

5190

AN:

41518

American (AMR)

AF:

0.322

AC:

4912

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.288

AC:

999

AN:

3466

East Asian (EAS)

AF:

0.458

AC:

2358

AN:

5150

South Asian (SAS)

AF:

0.313

AC:

1507

AN:

4818

European-Finnish (FIN)

AF:

0.215

AC:

2269

AN:

10574

Middle Eastern (MID)

AF:

0.264

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.223

AC:

15160

AN:

67916

Other (OTH)

AF:

0.259

AC:

546

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1255

2510

3765

5020

6275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.225

Hom.:

8740

Bravo

AF:

0.222

Asia WGS

AF:

0.369

AC:

1285

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.59

PhyloP100

4.0

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