Genetic Variant XR_947027.3:n.42-8745T>C (chr1-19874497-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_947027.3(LOC105376823):n.42-8745T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,952 control chromosomes in the GnomAD database, including 21,380 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 0.52 ( 21380 hom., cov: 31)

Consequence

LOC105376823
XR_947027.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75

Publications

18 publications found

Variant links:

Genes affected

LOC105376823 (HGNC:):

LOC105376823 links:

Genome browser will be placed here

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=-1.04).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376823	XR_947027.3 link	n.42-8745T>C		intron_variant	Intron 1 of 2
LOC105376823	XR_947028.3 link	n.42-8745T>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.522

AC:

79297

AN:

151832

Hom.:

21334

Cov.:

show subpopulations

Gnomad AFR

AF:

0.633

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.513

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.498

Gnomad OTH

AF:

0.502

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

GnomAD4 genome

AF:

0.523

AC:

79408

AN:

151952

Hom.:

21380

Cov.:

AF XY:

0.520

AC XY:

38589

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.633

AC:

26243

AN:

41452

American (AMR)

AF:

0.514

AC:

7848

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

1526

AN:

3470

East Asian (EAS)

AF:

0.270

AC:

1397

AN:

5166

South Asian (SAS)

AF:

0.340

AC:

1631

AN:

4804

European-Finnish (FIN)

AF:

0.511

AC:

5395

AN:

10568

Middle Eastern (MID)

AF:

0.432

AC:

126

AN:

292

European-Non Finnish (NFE)

AF:

0.498

AC:

33829

AN:

67920

Other (OTH)

AF:

0.498

AC:

1053

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1931

3863

5794

7726

9657

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

684

1368

2052

2736

3420

<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:

0.495

Hom.:

79302

Bravo

AF:

0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.33

(source)

DANN

Benign

0.32

PhyloP100

-1.8

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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