dbSNP rs1442855: LOC105374433:n.202+5618C>T (chr4-43321899-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_925266.3(LOC105374433):n.202+5618C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,794 control chromosomes in the GnomAD database, including 17,437 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 0.44 ( 17437 hom., cov: 32)

Consequence

LOC105374433
XR_925266.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

4 publications found

Variant links:

Genes affected

LOC105374433 (HGNC:):

LOC105374433 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 = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105374433	XR_925266.3 link	n.202+5618C>T	intron_variant	Intron 1 of 3
LOC105374433	XR_925267.3 link	n.202+5618C>T	intron_variant	Intron 1 of 2
LOC105374434	XR_925268.1 link	n.143+8655G>A	intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.439

AC:

66603

AN:

151674

Hom.:

17440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.736

Gnomad AMR

AF:

0.465

Gnomad ASJ

AF:

0.501

Gnomad EAS

AF:

0.141

Gnomad SAS

AF:

0.431

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.491

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

GnomAD4 genome

AF:

0.439

AC:

66596

AN:

151794

Hom.:

17437

Cov.:

AF XY:

0.433

AC XY:

32146

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.170

AC:

6998

AN:

41248

American (AMR)

AF:

0.465

AC:

7096

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.501

AC:

1737

AN:

3468

East Asian (EAS)

AF:

0.141

AC:

728

AN:

5162

South Asian (SAS)

AF:

0.433

AC:

2082

AN:

4810

European-Finnish (FIN)

AF:

0.540

AC:

5696

AN:

10554

Middle Eastern (MID)

AF:

0.582

AC:

170

AN:

292

European-Non Finnish (NFE)

AF:

0.594

AC:

40393

AN:

67970

Other (OTH)

AF:

0.486

AC:

1025

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1641

3282

4923

6564

8205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<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:

0.553

Hom.:

39170

Bravo

AF:

0.421

Asia WGS

AF:

0.262

AC:

916

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.085

(source)

DANN

Benign

0.49

PhyloP100

-1.2

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