rs7969932

chr12-64528407-C-T

Variant summary

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

The ENST00000541885.1(ENSG00000256199):n.307+4925G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,042 control chromosomes in the GnomAD database, including 24,990 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 0.57 (24990 hom., cov: 33)
• Consequence: ENST00000541885.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

Genes affected

(HGNC:):

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369803	XR_002957417.1	n.534+4925G>A		intron_variant, non_coding_transcript_variant
RASSF3	XM_047428711.1	c.125-13174C>T		intron_variant
RASSF3	XM_047428712.1	c.278-13174C>T		intron_variant
LOC105369803	XR_945026.3	n.793+4925G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000541885.1	n.307+4925G>A		intron_variant, non_coding_transcript_variant		3
RASSF3	ENST00000637125.1	c.170-13174C>T		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86067 AN: 151926 Hom.: 24984 Cov.: 33

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.566 AC: 86118 AN: 152042 Hom.: 24990 Cov.: 33 AF XY: 0.569 AC XY: 42302 AN XY: 74320

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.571

Alfa AF: 0.564 Hom.: 12605

Bravo AF: 0.570

Asia WGS AF: 0.753 AC: 2616 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	11
Dann	Benign	0.64

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7969932; hg19: chr12-64922187;