12-64641079-C-T

Position:

• chr12-64641079-C-T

Variant summary

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

The NM_178169.4(RASSF3):​c.111+30336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,884 control chromosomes in the GnomAD database, including 23,426 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 0.55 (23426 hom., cov: 31)
• Consequence: RASSF3 NM_178169.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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]

RASSF3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RASSF3	NM_178169.4	c.111+30336C>T		intron_variant		ENST00000542104.6	NP_835463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RASSF3	ENST00000542104.6	c.111+30336C>T		intron_variant		1	NM_178169.4	ENSP00000443021.1
RASSF3	ENST00000637125.1	c.295-43708C>T		intron_variant		5		ENSP00000490100.1
RASSF3	ENST00000283172.8	n.111+30336C>T		intron_variant		2		ENSP00000283172.4

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83836 AN: 151766 Hom.: 23417 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.552 AC: 83869 AN: 151884 Hom.: 23426 Cov.: 31 AF XY: 0.544 AC XY: 40404 AN XY: 74216

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.565

Alfa AF: 0.555 Hom.: 12100

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.5
DANN	Benign	0.78

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: rs2682724; hg19: chr12-65034859;