Genetic Variant XR_001744394.2:n.89+1162A>G (chr6-142034354-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_001744394.2(LOC107986654):n.89+1162A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,144 control chromosomes in the GnomAD database, including 34,552 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 0.65 ( 34552 hom., cov: 33)

Consequence

LOC107986654
XR_001744394.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396

Publications

1 publications found

Variant links:

Genes affected

LOC107986654 (HGNC:):

LOC107986654 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986654	XR_001744394.2 link	n.89+1162A>G		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.653

AC:

99295

AN:

152026

Hom.:

34485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.873

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.707

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.881

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.590

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.520

Gnomad OTH

AF:

0.643

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

GnomAD4 genome

AF:

0.653

AC:

99425

AN:

152144

Hom.:

34552

Cov.:

AF XY:

0.659

AC XY:

49001

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.873

AC:

36242

AN:

41526

American (AMR)

AF:

0.707

AC:

10820

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1248

AN:

3468

East Asian (EAS)

AF:

0.881

AC:

4559

AN:

5174

South Asian (SAS)

AF:

0.624

AC:

3005

AN:

4816

European-Finnish (FIN)

AF:

0.590

AC:

6235

AN:

10564

Middle Eastern (MID)

AF:

0.503

AC:

148

AN:

294

European-Non Finnish (NFE)

AF:

0.520

AC:

35359

AN:

67982

Other (OTH)

AF:

0.644

AC:

1361

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1606

3212

4819

6425

8031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<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:

0.624

Hom.:

9819

Bravo

AF:

0.677

Asia WGS

AF:

0.760

AC:

2640

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.44

(source)

DANN

Benign

0.36

PhyloP100

-0.40

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