dbSNP rs882845: RASSF4:c.138+151T>A (chr10-44971999-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 NM_032023.4(RASSF4):c.138+151T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 602,498 control chromosomes in the GnomAD database, including 103,039 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 0.51 ( 21999 hom., cov: 32)

Exomes 𝑓: 0.59 ( 81040 hom. )

Consequence

RASSF4
NM_032023.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

Publications

5 publications found

Variant links:

Genes affected

RASSF4 (HGNC:20793): (Ras association domain family member 4) The function of this gene has not yet been determined but may involve a role in tumor suppression. Alternative splicing of this gene results in several transcript variants; however, most of the variants have not been fully described. [provided by RefSeq, Jul 2008]

RASSF4 links:

DEPP1 (HGNC:23355): (DEPP autophagy regulator 1) The expression of this gene is induced by fasting as well as by progesterone. The protein encoded by this gene contains a t-synaptosome-associated protein receptor (SNARE) coiled-coil homology domain and a peroxisomal targeting signal. Production of the encoded protein leads to phosphorylation and activation of the transcription factor ELK1. [provided by RefSeq, Jul 2008]

DEPP1 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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032023.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RASSF4	NM_032023.4	MANE Select	c.138+151T>A		intron	N/A	NP_114412.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
RASSF4	ENST00000340258.10	TSL:1 MANE Select	c.138+151T>A	intron	N/A	ENSP00000339692.4	Q9H2L5-1
RASSF4	ENST00000489171.5	TSL:1	n.2144+151T>A	intron	N/A
RASSF4	ENST00000952763.1		c.138+151T>A	intron	N/A	ENSP00000622822.1

Frequencies

GnomAD3 genomes

AF:

0.508

AC:

77167

AN:

151930

Hom.:

21988

Cov.:

show subpopulations

Gnomad AFR

AF:

0.238

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.587

Gnomad EAS

AF:

0.336

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.500

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.541

GnomAD4 exome

AF:

0.589

AC:

265439

AN:

450448

Hom.:

81040

AF XY:

0.585

AC XY:

138325

AN XY:

236566

show subpopulations

African (AFR)

AF:

0.237

AC:

2945

AN:

12444

American (AMR)

AF:

0.603

AC:

11216

AN:

18596

Ashkenazi Jewish (ASJ)

AF:

0.581

AC:

7815

AN:

13454

East Asian (EAS)

AF:

0.362

AC:

11084

AN:

30578

South Asian (SAS)

AF:

0.496

AC:

22207

AN:

44770

European-Finnish (FIN)

AF:

0.673

AC:

20645

AN:

30670

Middle Eastern (MID)

AF:

0.559

AC:

1084

AN:

1940

European-Non Finnish (NFE)

AF:

0.637

AC:

173541

AN:

272244

Other (OTH)

AF:

0.579

AC:

14902

AN:

25752

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

4920

9840

14761

19681

24601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

854

1708

2562

3416

4270

<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:

0.508

AC:

77203

AN:

152050

Hom.:

21999

Cov.:

AF XY:

0.512

AC XY:

38068

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.238

AC:

9854

AN:

41474

American (AMR)

AF:

0.582

AC:

8887

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.587

AC:

2035

AN:

3468

East Asian (EAS)

AF:

0.337

AC:

1740

AN:

5170

South Asian (SAS)

AF:

0.489

AC:

2354

AN:

4814

European-Finnish (FIN)

AF:

0.682

AC:

7211

AN:

10572

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.638

AC:

43351

AN:

67954

Other (OTH)

AF:

0.545

AC:

1152

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1726

3451

5177

6902

8628

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<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:

0.444

Hom.:

1412

Bravo

AF:

0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

1.4

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over