dbSNP rs1020049: ENSG00000251574:n.328+94917G>T (chr5-104791941-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000503650.1(ENSG00000251574):n.328+94917G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,116 control chromosomes in the GnomAD database, including 1,115 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 0.12 ( 1115 hom., cov: 32)

Consequence

ENSG00000251574
ENST00000503650.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.35

Publications

3 publications found

Variant links:

Genes affected

ENSG00000251574 (HGNC:):

ENSG00000251574 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 = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000251574	ENST00000503650.1 link	n.328+94917G>T	intron_variant	Intron 2 of 2	3
ENSG00000253776	ENST00000523745.1 link	n.101-7365C>A	intron_variant	Intron 1 of 1	3
ENSG00000251574	ENST00000524336.5 link	n.190+94917G>T	intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17486

AN:

151998

Hom.:

1112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0972

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.0984

Gnomad ASJ

AF:

0.0885

Gnomad EAS

AF:

0.00674

Gnomad SAS

AF:

0.0681

Gnomad FIN

AF:

0.171

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.115

AC:

17510

AN:

152116

Hom.:

1115

Cov.:

AF XY:

0.113

AC XY:

8434

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.0976

AC:

4051

AN:

41500

American (AMR)

AF:

0.0981

AC:

1498

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0885

AC:

307

AN:

3468

East Asian (EAS)

AF:

0.00675

AC:

AN:

5184

South Asian (SAS)

AF:

0.0679

AC:

328

AN:

4828

European-Finnish (FIN)

AF:

0.171

AC:

1805

AN:

10568

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.134

AC:

9079

AN:

67980

Other (OTH)

AF:

0.110

AC:

233

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

771

1542

2314

3085

3856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

202

404

606

808

1010

<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:

0.117

Hom.:

1933

Bravo

AF:

0.109

Asia WGS

AF:

0.0510

AC:

182

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

0.10

(source)

DANN

Benign

0.76

PhyloP100

-2.4

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