Genetic Variant LOC105376214:n.721-77978dupA (chr9-108131271-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_001746881.2(LOC105376214):n.721-77978dupA variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.69 ( 36700 hom., cov: 0)

Consequence

LOC105376214
XR_001746881.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.67

Publications

3 publications found

Variant links:

Genes affected

LOC105376214 (HGNC:):

LOC105376214 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376214	XR_001746881.2 link	n.721-77978dupA	intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2 link	n.721-77978dupA	intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1 link	n.721-77978dupA	intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104840

AN:

151932

Hom.:

36642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.761

Gnomad AMI

AF:

0.644

Gnomad AMR

AF:

0.670

Gnomad ASJ

AF:

0.636

Gnomad EAS

AF:

0.957

Gnomad SAS

AF:

0.856

Gnomad FIN

AF:

0.659

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.628

Gnomad OTH

AF:

0.682

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

GnomAD4 genome

AF:

0.690

AC:

104958

AN:

152050

Hom.:

36700

Cov.:

AF XY:

0.698

AC XY:

51897

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.762

AC:

31591

AN:

41474

American (AMR)

AF:

0.670

AC:

10232

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.636

AC:

2205

AN:

3466

East Asian (EAS)

AF:

0.957

AC:

4953

AN:

5178

South Asian (SAS)

AF:

0.856

AC:

4128

AN:

4822

European-Finnish (FIN)

AF:

0.659

AC:

6954

AN:

10558

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.628

AC:

42667

AN:

67966

Other (OTH)

AF:

0.684

AC:

1445

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1656

3311

4967

6622

8278

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<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:

0.672

Hom.:

4220

Bravo

AF:

0.692

Asia WGS

AF:

0.899

AC:

3121

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.7

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