Genetic Variant LOC112268032:n.87416754G>C (chr9-87416754-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 variant allele was found at a frequency of 0.0726 in 152,002 control chromosomes in the GnomAD database, including 511 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 0.073 ( 511 hom., cov: 31)

Consequence

LOC112268032
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.78

Publications

6 publications found

Variant links:

Genes affected

LOC112268032 (HGNC:):

LOC112268032 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 (NFE) allele frequency at 95% confidence interval = 0.0936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268032		n.87416754G>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289166	ENST00000804137.1 link	n.32+6299C>G		intron_variant	Intron 1 of 1
ENSG00000289166	ENST00000804138.1 link	n.32+6299C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0726

AC:

11026

AN:

151884

Hom.:

509

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0490

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0697

Gnomad ASJ

AF:

0.0987

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0162

Gnomad FIN

AF:

0.0764

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0955

Gnomad OTH

AF:

0.0662

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

GnomAD4 genome

AF:

0.0726

AC:

11037

AN:

152002

Hom.:

511

Cov.:

AF XY:

0.0691

AC XY:

5137

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.0492

AC:

2036

AN:

41394

American (AMR)

AF:

0.0697

AC:

1065

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0987

AC:

342

AN:

3466

East Asian (EAS)

AF:

0.000193

AC:

AN:

5176

South Asian (SAS)

AF:

0.0162

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.0764

AC:

808

AN:

10572

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0955

AC:

6495

AN:

67996

Other (OTH)

AF:

0.0655

AC:

138

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

451

902

1353

1804

2255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<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:

0.0876

Hom.:

394

Bravo

AF:

0.0712

Asia WGS

AF:

0.0120

AC:

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

5.7

(source)

DANN

Benign

0.47

PhyloP100

1.8

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