rs1147098

chr12-64621464-G-A

Variant summary

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

The NM_178169.4(RASSF3):c.111+10721G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,892 control chromosomes in the GnomAD database, including 19,033 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 0.50 (19033 hom., cov: 31)
• Consequence: RASSF3 NM_178169.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

Genes affected

RASSF3 (HGNC:14271): (Ras association domain family member 3) The RAS oncogene (MIM 190020) is mutated in nearly one-third of all human cancers. Members of the RAS superfamily are plasma membrane GTP-binding proteins that modulate intracellular signal transduction pathways. A subfamily of RAS effectors, including RASSF3, share a RAS association (RA) domain.[supplied by OMIM, Jul 2003]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASSF3	NM_178169.4	c.111+10721G>A		intron_variant		ENST00000542104.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASSF3	ENST00000542104.6	c.111+10721G>A		intron_variant		1	NM_178169.4	P2
RASSF3	ENST00000637125.1	c.295-63323G>A		intron_variant		5		A2
RASSF3	ENST00000283172.8	c.111+10721G>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75624 AN: 151776 Hom.: 19019 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.488

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.498 AC: 75669 AN: 151892 Hom.: 19033 Cov.: 31 AF XY: 0.491 AC XY: 36476 AN XY: 74230

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.487

Alfa AF: 0.515 Hom.: 40497

Bravo AF: 0.499

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	13
Dann	Benign	0.76

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: rs1147098; hg19: chr12-65015244;