Genetic Variant NR_130785.1:n.80-44056C>G (chr5-114712287-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NR_130785.1(LOC101927078):n.80-44056C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 151,978 control chromosomes in the GnomAD database, including 185 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 0.034 ( 185 hom., cov: 32)

Consequence

LOC101927078
NR_130785.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.619

Publications

0 publications found

Variant links:

Genes affected

LOC101927078 (HGNC:):

LOC101927078 links:

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new If you want to explore the variant's impact on the transcript NR_130785.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_130785.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927078	NR_130785.1		n.80-44056C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes

AF:

0.0343

AC:

5207

AN:

151860

Hom.:

182

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0831

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0265

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.0340

Gnomad SAS

AF:

0.0533

Gnomad FIN

AF:

0.000379

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0116

Gnomad OTH

AF:

0.0292

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

GnomAD4 genome

AF:

0.0343

AC:

5219

AN:

151978

Hom.:

185

Cov.:

AF XY:

0.0337

AC XY:

2505

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.0831

AC:

3442

AN:

41440

American (AMR)

AF:

0.0264

AC:

402

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

AN:

3472

East Asian (EAS)

AF:

0.0343

AC:

177

AN:

5158

South Asian (SAS)

AF:

0.0525

AC:

253

AN:

4816

European-Finnish (FIN)

AF:

0.000379

AC:

AN:

10554

Middle Eastern (MID)

AF:

0.0411

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0116

AC:

789

AN:

67974

Other (OTH)

AF:

0.0326

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

244

488

732

976

1220

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

112

168

224

280

<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:

0.00630

Hom.:

Bravo

AF:

0.0374

Asia WGS

AF:

0.0550

AC:

190

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.33

(source)

DANN

Benign

0.47

PhyloP100

-0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over