Genetic Variant NR_105012.1:n.171-30018T>C (chr5-77928842-T-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_105012.1(LOC101929154):n.171-30018T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,956 control chromosomes in the GnomAD database, including 29,281 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 ( 29281 hom., cov: 30)

Consequence

LOC101929154
NR_105012.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.587

Publications

4 publications found

Variant links:

Genes affected

LOC101929154 (HGNC:):

LOC101929154 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929154	NR_105012.1 link	n.171-30018T>C		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.600

AC:

91103

AN:

151838

Hom.:

29236

Cov.:

show subpopulations

Gnomad AFR

AF:

0.834

Gnomad AMI

AF:

0.273

Gnomad AMR

AF:

0.677

Gnomad ASJ

AF:

0.558

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.458

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.547

Gnomad NFE

AF:

0.488

Gnomad OTH

AF:

0.620

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

GnomAD4 genome

AF:

0.600

AC:

91208

AN:

151956

Hom.:

29281

Cov.:

AF XY:

0.597

AC XY:

44358

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.834

AC:

34573

AN:

41468

American (AMR)

AF:

0.677

AC:

10343

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

1933

AN:

3466

East Asian (EAS)

AF:

0.465

AC:

2391

AN:

5142

South Asian (SAS)

AF:

0.457

AC:

2200

AN:

4814

European-Finnish (FIN)

AF:

0.463

AC:

4885

AN:

10546

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.488

AC:

33169

AN:

67930

Other (OTH)

AF:

0.620

AC:

1306

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1634

3269

4903

6538

8172

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.533

Hom.:

37920

Bravo

AF:

0.633

Asia WGS

AF:

0.519

AC:

1806

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.24

(source)

DANN

Benign

0.38

PhyloP100

-0.59

Splicing

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

Publications

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NR_105012.1:n.171-30018T>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