dbSNP rs3814568: RASSF4:c.807+58G>A (chr10-44991127-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 NM_032023.4(RASSF4):c.807+58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0502 in 1,527,448 control chromosomes in the GnomAD database, including 2,845 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 0.041 ( 208 hom., cov: 33)

Exomes 𝑓: 0.051 ( 2637 hom. )

Consequence

RASSF4
NM_032023.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.01

Publications

2 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:

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=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF4	NM_032023.4 link	c.807+58G>A		intron_variant	Intron 9 of 10	ENST00000340258.10	NP_114412.2	Q9H2L5-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF4	ENST00000340258.10 link	c.807+58G>A		intron_variant	Intron 9 of 10	1	NM_032023.4	ENSP00000339692.4		Q9H2L5-1

Frequencies

GnomAD3 genomes

AF:

0.0414

AC:

6292

AN:

152094

Hom.:

210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0101

Gnomad AMI

AF:

0.0879

Gnomad AMR

AF:

0.0373

Gnomad ASJ

AF:

0.0314

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.0371

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0447

Gnomad OTH

AF:

0.0441

GnomAD2 exomes

AF:

0.0632

AC:

12892

AN:

203962

AF XY:

0.0680

show subpopulations

Gnomad AFR exome

AF:

0.00924

Gnomad AMR exome

AF:

0.0288

Gnomad ASJ exome

AF:

0.0363

Gnomad EAS exome

AF:

0.163

Gnomad FIN exome

AF:

0.0402

Gnomad NFE exome

AF:

0.0445

Gnomad OTH exome

AF:

0.0579

GnomAD4 exome

AF:

0.0512

AC:

70413

AN:

1375236

Hom.:

2637

Cov.:

AF XY:

0.0540

AC XY:

36655

AN XY:

679102

show subpopulations

African (AFR)

AF:

0.00680

AC:

213

AN:

31322

American (AMR)

AF:

0.0281

AC:

1072

AN:

38166

Ashkenazi Jewish (ASJ)

AF:

0.0359

AC:

834

AN:

23248

East Asian (EAS)

AF:

0.141

AC:

5450

AN:

38594

South Asian (SAS)

AF:

0.149

AC:

11774

AN:

78876

European-Finnish (FIN)

AF:

0.0403

AC:

1707

AN:

42310

Middle Eastern (MID)

AF:

0.0301

AC:

141

AN:

4678

European-Non Finnish (NFE)

AF:

0.0435

AC:

46139

AN:

1061354

Other (OTH)

AF:

0.0544

AC:

3083

AN:

56688

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

2929

5857

8786

11714

14643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1930

3860

5790

7720

9650

<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:

0.0413

AC:

6284

AN:

152212

Hom.:

208

Cov.:

AF XY:

0.0441

AC XY:

3279

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0101

AC:

420

AN:

41552

American (AMR)

AF:

0.0373

AC:

570

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0314

AC:

109

AN:

3468

East Asian (EAS)

AF:

0.150

AC:

774

AN:

5152

South Asian (SAS)

AF:

0.164

AC:

788

AN:

4814

European-Finnish (FIN)

AF:

0.0371

AC:

393

AN:

10606

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0448

AC:

3044

AN:

68010

Other (OTH)

AF:

0.0436

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

297

595

892

1190

1487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0403

Hom.:

Bravo

AF:

0.0376

Asia WGS

AF:

0.141

AC:

488

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.30

(source)

DANN

Benign

0.52

PhyloP100

-1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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