Genetic Variant REL-DT:n.403+4526C>T (chr2-60839531-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000439412.6(REL-DT):n.403+4526C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,056 control chromosomes in the GnomAD database, including 37,430 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 0.69 ( 37430 hom., cov: 31)

Consequence

REL-DT
ENST00000439412.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.356

Publications

51 publications found

Variant links:

Genes affected

REL-DT (HGNC:49572): (REL divergent transcript)

REL-DT 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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
REL-DT	ENST00000439412.6 link	n.403+4526C>T	intron_variant	Intron 3 of 3	4
REL-DT	ENST00000748843.1 link	n.363+4526C>T	intron_variant	Intron 3 of 4
REL-DT	ENST00000748844.1 link	n.248+4526C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104876

AN:

151938

Hom.:

37375

Cov.:

show subpopulations

Gnomad AFR

AF:

0.812

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.726

Gnomad ASJ

AF:

0.698

Gnomad EAS

AF:

0.979

Gnomad SAS

AF:

0.884

Gnomad FIN

AF:

0.567

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.660

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

GnomAD4 genome

AF:

0.690

AC:

104991

AN:

152056

Hom.:

37430

Cov.:

AF XY:

0.695

AC XY:

51620

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.811

AC:

33673

AN:

41496

American (AMR)

AF:

0.727

AC:

11102

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.698

AC:

2422

AN:

3468

East Asian (EAS)

AF:

0.979

AC:

5072

AN:

5180

South Asian (SAS)

AF:

0.884

AC:

4265

AN:

4826

European-Finnish (FIN)

AF:

0.567

AC:

5966

AN:

10530

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.594

AC:

40343

AN:

67962

Other (OTH)

AF:

0.665

AC:

1406

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1572

3144

4716

6288

7860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.634

Hom.:

140760

Bravo

AF:

0.705

Asia WGS

AF:

0.920

AC:

3199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.88

(source)

DANN

Benign

0.52

PhyloP100

-0.36

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