Genetic Variant RELL1:c.89-33T>C (chr4-37649533-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 NM_001085400.2(RELL1):c.89-33T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,577,004 control chromosomes in the GnomAD database, including 100,447 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 0.31 ( 7720 hom., cov: 33)

Exomes 𝑓: 0.36 ( 92727 hom. )

Consequence

RELL1
NM_001085400.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

Publications

8 publications found

Variant links:

Genes affected

RELL1 (HGNC:27379): (RELT like 1) Involved in positive regulation of p38MAPK cascade. Located in microtubule cytoskeleton and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

RELL1 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=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RELL1	NM_001085400.2 link	c.89-33T>C		intron_variant	Intron 1 of 6	ENST00000454158.7	NP_001078869.1	Q8IUW5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
RELL1	ENST00000454158.7 link	c.89-33T>C	intron_variant	Intron 1 of 6	5	NM_001085400.2	ENSP00000398778.2	Q8IUW5
RELL1	ENST00000314117.8 link	c.89-33T>C	intron_variant	Intron 1 of 6	1		ENSP00000313385.4	Q8IUW5
RELL1	ENST00000512114.1 link	c.152-33T>C	intron_variant	Intron 1 of 4	3		ENSP00000424031.1	D6RBN9

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47884

AN:

152062

Hom.:

7720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.271

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.370

Gnomad OTH

AF:

0.326

GnomAD2 exomes

AF:

0.325

AC:

79679

AN:

245468

AF XY:

0.326

show subpopulations

Gnomad AFR exome

AF:

0.246

Gnomad AMR exome

AF:

0.227

Gnomad ASJ exome

AF:

0.412

Gnomad EAS exome

AF:

0.311

Gnomad FIN exome

AF:

0.288

Gnomad NFE exome

AF:

0.378

Gnomad OTH exome

AF:

0.345

GnomAD4 exome

AF:

0.357

AC:

509005

AN:

1424824

Hom.:

92727

Cov.:

AF XY:

0.355

AC XY:

252238

AN XY:

710406

show subpopulations

African (AFR)

AF:

0.242

AC:

7928

AN:

32704

American (AMR)

AF:

0.235

AC:

10420

AN:

44386

Ashkenazi Jewish (ASJ)

AF:

0.410

AC:

10517

AN:

25640

East Asian (EAS)

AF:

0.298

AC:

11766

AN:

39528

South Asian (SAS)

AF:

0.278

AC:

23621

AN:

85120

European-Finnish (FIN)

AF:

0.294

AC:

15660

AN:

53232

Middle Eastern (MID)

AF:

0.376

AC:

1642

AN:

4364

European-Non Finnish (NFE)

AF:

0.377

AC:

406965

AN:

1080876

Other (OTH)

AF:

0.347

AC:

20486

AN:

58974

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

16739

33478

50218

66957

83696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12608

25216

37824

50432

63040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.315

AC:

47905

AN:

152180

Hom.:

7720

Cov.:

AF XY:

0.308

AC XY:

22884

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.246

AC:

10221

AN:

41514

American (AMR)

AF:

0.272

AC:

4153

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.422

AC:

1466

AN:

3472

East Asian (EAS)

AF:

0.284

AC:

1469

AN:

5174

South Asian (SAS)

AF:

0.282

AC:

1361

AN:

4826

European-Finnish (FIN)

AF:

0.274

AC:

2906

AN:

10588

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.370

AC:

25175

AN:

68002

Other (OTH)

AF:

0.324

AC:

682

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1768

3535

5303

7070

8838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

492

984

1476

1968

2460

<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:

0.337

Hom.:

9310

Bravo

AF:

0.315

Asia WGS

AF:

0.261

AC:

906

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.052

(source)

DANN

Benign

0.26

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over