Genetic Variant LOC105376815:n.552-25728G>A (chr1-19022787-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_947015.2(LOC105376815):n.552-25728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 150,808 control chromosomes in the GnomAD database, including 7,860 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 0.30 ( 7860 hom., cov: 30)

Consequence

LOC105376815
XR_947015.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.447

Publications

4 publications found

Variant links:

Genes affected

LOC105376815 (HGNC:):

LOC105376815 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376815	XR_947015.2 link	n.552-25728G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45043

AN:

150710

Hom.:

7855

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.421

Gnomad ASJ

AF:

0.397

Gnomad EAS

AF:

0.685

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.316

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.323

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

GnomAD4 genome

AF:

0.299

AC:

45067

AN:

150808

Hom.:

7860

Cov.:

AF XY:

0.304

AC XY:

22411

AN XY:

73600

show subpopulations

African (AFR)

AF:

0.153

AC:

6259

AN:

40990

American (AMR)

AF:

0.422

AC:

6398

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.397

AC:

1372

AN:

3456

East Asian (EAS)

AF:

0.685

AC:

3512

AN:

5128

South Asian (SAS)

AF:

0.310

AC:

1471

AN:

4752

European-Finnish (FIN)

AF:

0.316

AC:

3233

AN:

10236

Middle Eastern (MID)

AF:

0.271

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.321

AC:

21769

AN:

67776

Other (OTH)

AF:

0.323

AC:

679

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1466

2933

4399

5866

7332

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.309

Hom.:

4001

Bravo

AF:

0.303

Asia WGS

AF:

0.477

AC:

1657

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

0.45

Splicing

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

Publications

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1-19022787-C-T

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