dbSNP rs9312601: LOC124900817:n.912+1893T>A (chr4-176445891-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_007058376.1(LOC124900817):n.912+1893T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,960 control chromosomes in the GnomAD database, including 27,998 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 ( 27998 hom., cov: 32)

Consequence

LOC124900817
XR_007058376.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.181

Publications

3 publications found

Variant links:

Genes affected

LOC124900817 (HGNC:):

LOC124900817 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC124900817	XR_007058376.1 link	n.912+1893T>A	intron_variant	Intron 1 of 3
LOC124900817	XR_007058377.1 link	n.414+1893T>A	intron_variant	Intron 3 of 3
LOC124900817	XR_007058378.1 link	n.294+1893T>A	intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.602

AC:

91479

AN:

151842

Hom.:

27989

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.742

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.758

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.548

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.644

Gnomad OTH

AF:

0.615

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

GnomAD4 genome

AF:

0.602

AC:

91512

AN:

151960

Hom.:

27998

Cov.:

AF XY:

0.600

AC XY:

44578

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.540

AC:

22389

AN:

41436

American (AMR)

AF:

0.613

AC:

9356

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.758

AC:

2629

AN:

3468

East Asian (EAS)

AF:

0.373

AC:

1928

AN:

5166

South Asian (SAS)

AF:

0.547

AC:

2636

AN:

4816

European-Finnish (FIN)

AF:

0.632

AC:

6674

AN:

10566

Middle Eastern (MID)

AF:

0.738

AC:

217

AN:

294

European-Non Finnish (NFE)

AF:

0.644

AC:

43723

AN:

67936

Other (OTH)

AF:

0.609

AC:

1283

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1828

3656

5483

7311

9139

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.613

Hom.:

3582

Bravo

AF:

0.597

Asia WGS

AF:

0.437

AC:

1520

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.7

(source)

DANN

Benign

0.80

PhyloP100

0.18

Splicing

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

Publications

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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