rs869156

chr10-44983604-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASSF4	NM_032023.4	c.282-418C>A		intron_variant		ENST00000340258.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASSF4	ENST00000340258.10	c.282-418C>A		intron_variant		1	NM_032023.4	P1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80252 AN: 151914 Hom.: 22884 Cov.: 33

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.: 0 AF XY: 0.585 AC XY: 12659 AN XY: 21656

Gnomad4 AFR exome AF: 0.284

Gnomad4 AMR exome AF: 0.598

Gnomad4 ASJ exome AF: 0.583

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.498

Gnomad4 FIN exome AF: 0.654

Gnomad4 NFE exome AF: 0.635

Gnomad4 OTH exome AF: 0.598

GnomAD4 genome AF: 0.528 AC: 80286 AN: 152032 Hom.: 22897 Cov.: 33 AF XY: 0.531 AC XY: 39452 AN XY: 74302

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.510

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.565

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.4
Dann	Benign	0.58

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

LitVar

Other links and lift over

dbSNP: rs869156; hg19: chr10-45479052;