Genetic Variant LOC105376214:n.721-56733G>A (chr9-108110027-C-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_001746881.2(LOC105376214):n.721-56733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,034 control chromosomes in the GnomAD database, including 8,082 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 0.32 ( 8082 hom., cov: 32)

Consequence

LOC105376214
XR_001746881.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.12

Publications

9 publications found

Variant links:

Genes affected

LOC105376214 (HGNC:):

LOC105376214 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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376214	XR_001746881.2 link	n.721-56733G>A	intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2 link	n.721-56733G>A	intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1 link	n.721-56733G>A	intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48451

AN:

151916

Hom.:

8082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.619

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.0684

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.347

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

GnomAD4 genome

AF:

0.319

AC:

48470

AN:

152034

Hom.:

8082

Cov.:

AF XY:

0.315

AC XY:

23384

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.291

AC:

12052

AN:

41478

American (AMR)

AF:

0.302

AC:

4621

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

881

AN:

3470

East Asian (EAS)

AF:

0.0682

AC:

352

AN:

5160

South Asian (SAS)

AF:

0.357

AC:

1718

AN:

4806

European-Finnish (FIN)

AF:

0.312

AC:

3298

AN:

10558

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.355

AC:

24159

AN:

67968

Other (OTH)

AF:

0.343

AC:

724

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1653

3306

4959

6612

8265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.335

Hom.:

33220

Bravo

AF:

0.314

Asia WGS

AF:

0.231

AC:

804

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

(source)

DANN

Benign

0.56

PhyloP100

2.1

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