Genetic Variant LOC107986324:n.76+26756G>T (chr4-159567154-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_001741911.2(LOC107986324):n.76+26756G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,888 control chromosomes in the GnomAD database, including 16,132 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 0.45 ( 16132 hom., cov: 31)

Consequence

LOC107986324
XR_001741911.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700

Publications

2 publications found

Variant links:

Genes affected

LOC107986324 (HGNC:):

LOC107986324 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986324	XR_001741911.2 link	n.76+26756G>T		intron_variant	Intron 1 of 2
LOC107986324	XR_001741912.2 link	n.146+18651G>T		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68620

AN:

151770

Hom.:

16114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.466

Gnomad AMR

AF:

0.590

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.712

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.394

Gnomad NFE

AF:

0.414

Gnomad OTH

AF:

0.462

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

GnomAD4 genome

AF:

0.452

AC:

68686

AN:

151888

Hom.:

16132

Cov.:

AF XY:

0.458

AC XY:

34017

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.435

AC:

18010

AN:

41410

American (AMR)

AF:

0.590

AC:

8999

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.505

AC:

1752

AN:

3468

East Asian (EAS)

AF:

0.713

AC:

3681

AN:

5162

South Asian (SAS)

AF:

0.362

AC:

1745

AN:

4816

European-Finnish (FIN)

AF:

0.458

AC:

4831

AN:

10558

Middle Eastern (MID)

AF:

0.400

AC:

116

AN:

290

European-Non Finnish (NFE)

AF:

0.414

AC:

28146

AN:

67920

Other (OTH)

AF:

0.465

AC:

982

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1874

3748

5623

7497

9371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.437

Hom.:

2205

Bravo

AF:

0.465

Asia WGS

AF:

0.547

AC:

1900

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.9

(source)

DANN

Benign

0.31

PhyloP100

-0.070

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