Genetic Variant LOC105376214:n.721-97231C>G (chr9-108150525-G-C) – 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.721-97231C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,962 control chromosomes in the GnomAD database, including 6,580 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 0.29 ( 6580 hom., cov: 33)

Consequence

LOC105376214
XR_001746881.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.785

Publications

4 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105376214	XR_001746881.2 link	n.721-97231C>G	intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2 link	n.721-97231C>G	intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1 link	n.721-97231C>G	intron_variant	Intron 4 of 5

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.293

AC:

44426

AN:

151844

Hom.:

6570

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.285

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.283

Gnomad NFE

AF:

0.281

Gnomad OTH

AF:

0.280

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

GnomAD4 genome

AF:

0.293

AC:

44465

AN:

151962

Hom.:

6580

Cov.:

AF XY:

0.300

AC XY:

22249

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.290

AC:

12034

AN:

41436

American (AMR)

AF:

0.236

AC:

3609

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.285

AC:

990

AN:

3468

East Asian (EAS)

AF:

0.463

AC:

2389

AN:

5156

South Asian (SAS)

AF:

0.388

AC:

1869

AN:

4816

European-Finnish (FIN)

AF:

0.333

AC:

3509

AN:

10526

Middle Eastern (MID)

AF:

0.281

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.281

AC:

19088

AN:

67974

Other (OTH)

AF:

0.276

AC:

584

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1648

3296

4943

6591

8239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

446

892

1338

1784

2230

<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:

0.170

Hom.:

330

Bravo

AF:

0.285

Asia WGS

AF:

0.379

AC:

1319

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.2

(source)

DANN

Benign

0.66

PhyloP100

0.79

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