Genetic Variant LOC107986665:n.160776055A>G (chr6-160776055-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 variant allele was found at a frequency of 0.6 in 152,014 control chromosomes in the GnomAD database, including 28,031 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 0.60 ( 28031 hom., cov: 32)

Consequence

LOC107986665
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.348

Publications

6 publications found

Variant links:

Genes affected

LOC107986665 (HGNC:):

LOC107986665 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986665		n.160776055A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000274903	ENST00000619095.1 link	n.45+2023A>G	intron_variant	Intron 1 of 1	6
ENSG00000303572	ENST00000795697.1 link	n.325+305T>C	intron_variant	Intron 2 of 2
ENSG00000303572	ENST00000795698.1 link	n.299+305T>C	intron_variant	Intron 2 of 2
ENSG00000303572	ENST00000795699.1 link	n.*8T>C	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91146

AN:

151896

Hom.:

28000

Cov.:

show subpopulations

Gnomad AFR

AF:

0.637

Gnomad AMI

AF:

0.565

Gnomad AMR

AF:

0.686

Gnomad ASJ

AF:

0.506

Gnomad EAS

AF:

0.982

Gnomad SAS

AF:

0.718

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.622

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

GnomAD4 genome

AF:

0.600

AC:

91227

AN:

152014

Hom.:

28031

Cov.:

AF XY:

0.607

AC XY:

45092

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.637

AC:

26399

AN:

41470

American (AMR)

AF:

0.687

AC:

10504

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.506

AC:

1756

AN:

3470

East Asian (EAS)

AF:

0.982

AC:

5070

AN:

5164

South Asian (SAS)

AF:

0.716

AC:

3453

AN:

4822

European-Finnish (FIN)

AF:

0.533

AC:

5620

AN:

10546

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.536

AC:

36402

AN:

67934

Other (OTH)

AF:

0.626

AC:

1323

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1841

3682

5523

7364

9205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.572

Hom.:

39488

Bravo

AF:

0.613

Asia WGS

AF:

0.834

AC:

2894

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

2.6

(source)

DANN

Benign

0.59

PhyloP100

0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr6-160776055-A-G

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