Genetic Variant LOC101927078:n.80-23913C>G (chr5-114692144-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 NR_130785.1(LOC101927078):n.80-23913C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 150,004 control chromosomes in the GnomAD database, including 40,095 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 0.73 ( 40095 hom., cov: 25)

Consequence

LOC101927078
NR_130785.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0640

Publications

1 publications found

Variant links:

COSMIC-nc: COSV60184635

Genes affected

LOC101927078 (HGNC:):

LOC101927078 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927078	NR_130785.1 link	n.80-23913C>G		intron_variant	Intron 1 of 12

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.726

AC:

108798

AN:

149902

Hom.:

40060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.832

Gnomad AMI

AF:

0.823

Gnomad AMR

AF:

0.652

Gnomad ASJ

AF:

0.786

Gnomad EAS

AF:

0.517

Gnomad SAS

AF:

0.658

Gnomad FIN

AF:

0.745

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.690

Gnomad OTH

AF:

0.750

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

GnomAD4 genome

AF:

0.726

AC:

108875

AN:

150004

Hom.:

40095

Cov.:

AF XY:

0.724

AC XY:

52893

AN XY:

73062

show subpopulations

African (AFR)

AF:

0.832

AC:

33953

AN:

40824

American (AMR)

AF:

0.652

AC:

9854

AN:

15124

Ashkenazi Jewish (ASJ)

AF:

0.786

AC:

2721

AN:

3460

East Asian (EAS)

AF:

0.517

AC:

2621

AN:

5068

South Asian (SAS)

AF:

0.657

AC:

3111

AN:

4732

European-Finnish (FIN)

AF:

0.745

AC:

7371

AN:

9894

Middle Eastern (MID)

AF:

0.863

AC:

252

AN:

292

European-Non Finnish (NFE)

AF:

0.690

AC:

46689

AN:

67622

Other (OTH)

AF:

0.748

AC:

1556

AN:

2080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

1402

2804

4205

5607

7009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.603

Hom.:

1718

Bravo

AF:

0.726

Asia WGS

AF:

0.563

AC:

1962

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

(source)

DANN

Benign

0.44

PhyloP100

0.064

Splicing

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

Publications

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5-114692144-G-C

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