dbSNP rs869156: RASSF4:c.282-418C>A (chr10-44983604-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 NM_032023.4(RASSF4):c.282-418C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 193,048 control chromosomes in the GnomAD database, including 30,539 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 0.53 ( 22897 hom., cov: 33)

Exomes 𝑓: 0.60 ( 7642 hom. )

Consequence

RASSF4
NM_032023.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.170

Publications

3 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 (NFE) allele frequency at 95% confidence interval = 0.635 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.282-418C>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.282-418C>A	intron	N/A	ENSP00000339692.4	Q9H2L5-1
RASSF4	ENST00000489171.5	TSL:1	n.2288-418C>A	intron	N/A
RASSF4	ENST00000952763.1		c.396-292C>A	intron	N/A	ENSP00000622822.1

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80252

AN:

151914

Hom.:

22884

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.598

Gnomad ASJ

AF:

0.603

Gnomad EAS

AF:

0.347

Gnomad SAS

AF:

0.511

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.640

Gnomad OTH

AF:

0.561

GnomAD4 exome

AF:

0.596

AC:

24454

AN:

41016

Hom.:

7642

Cov.:

AF XY:

0.585

AC XY:

12659

AN XY:

21656

show subpopulations

African (AFR)

AF:

0.284

AC:

164

AN:

578

American (AMR)

AF:

0.598

AC:

1547

AN:

2588

Ashkenazi Jewish (ASJ)

AF:

0.583

AC:

512

AN:

878

East Asian (EAS)

AF:

0.318

AC:

390

AN:

1226

South Asian (SAS)

AF:

0.498

AC:

2927

AN:

5876

European-Finnish (FIN)

AF:

0.654

AC:

1183

AN:

1808

Middle Eastern (MID)

AF:

0.536

AC:

AN:

168

European-Non Finnish (NFE)

AF:

0.635

AC:

16297

AN:

25648

Other (OTH)

AF:

0.598

AC:

1344

AN:

2246

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

451

902

1353

1804

2255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

224

336

448

560

<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:

0.528

AC:

80286

AN:

152032

Hom.:

22897

Cov.:

AF XY:

0.531

AC XY:

39452

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.303

AC:

12577

AN:

41472

American (AMR)

AF:

0.598

AC:

9132

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.603

AC:

2093

AN:

3470

East Asian (EAS)

AF:

0.348

AC:

1793

AN:

5158

South Asian (SAS)

AF:

0.510

AC:

2453

AN:

4808

European-Finnish (FIN)

AF:

0.663

AC:

7010

AN:

10574

Middle Eastern (MID)

AF:

0.534

AC:

157

AN:

294

European-Non Finnish (NFE)

AF:

0.640

AC:

43491

AN:

67964

Other (OTH)

AF:

0.565

AC:

1188

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1798

3596

5394

7192

8990

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

706

1412

2118

2824

3530

<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:

0.574

Hom.:

4143

Bravo

AF:

0.514

Asia WGS

AF:

0.447

AC:

1555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.4

(source)

DANN

Benign

0.58

PhyloP100

-0.17

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