Genetic Variant ENSG00000302860:n.303+2180C>A (chr4-11546343-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_188483.1(LOC107986178):n.191+2180C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,250 control chromosomes in the GnomAD database, including 942 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 0.099 ( 942 hom., cov: 32)

Consequence

LOC107986178
NR_188483.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.591

Publications

3 publications found

Variant links:

Genes affected

ENSG00000302860 (HGNC:):

ENSG00000302860 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986178	NR_188483.1 link	n.191+2180C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302860	ENST00000790104.1 link	n.303+2180C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0989

AC:

15050

AN:

152132

Hom.:

944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0292

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.0588

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.106

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

GnomAD4 genome

AF:

0.0989

AC:

15052

AN:

152250

Hom.:

942

Cov.:

AF XY:

0.0988

AC XY:

7351

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0292

AC:

1212

AN:

41564

American (AMR)

AF:

0.190

AC:

2902

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

479

AN:

3468

East Asian (EAS)

AF:

0.105

AC:

542

AN:

5170

South Asian (SAS)

AF:

0.148

AC:

715

AN:

4826

European-Finnish (FIN)

AF:

0.0588

AC:

623

AN:

10600

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8244

AN:

68016

Other (OTH)

AF:

0.106

AC:

224

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

702

1405

2107

2810

3512

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.121

Hom.:

1849

Bravo

AF:

0.105

Asia WGS

AF:

0.118

AC:

412

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.67

(source)

DANN

Benign

0.59

PhyloP100

-0.59

Splicing

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

Publications

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4-11546343-C-A

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