rs829837

Positions:

• chr12-25968797-C-T

Variant summary

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

The NM_001394098.1(RASSF8):​c.-203+9649C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 152,156 control chromosomes in the GnomAD database, including 879 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 0.084 (879 hom., cov: 33)
• Consequence: RASSF8 NM_001394098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

RASSF8 (HGNC:13232): (Ras association domain family member 8) This gene encodes a member of the Ras-assocation domain family (RASSF) of tumor suppressor proteins. This gene is essential for maintaining adherens junction function in epithelial cells and has a role in epithelial cell migration. It is a lung tumor suppressor gene candidate. A chromosomal translocation t(12;22)(p11.2;q13.3) leading to the fusion of this gene and the FBLN1 gene is found in a complex type of synpolydactyly. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASSF8	NM_001394098.1	c.-203+9649C>T		intron_variant		ENST00000689635.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASSF8	ENST00000689635.1	c.-203+9649C>T		intron_variant			NM_001394098.1	P1

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12765 AN: 152036 Hom.: 869 Cov.: 33

Gnomad AFR AF: 0.0791

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0840 AC: 12783 AN: 152156 Hom.: 879 Cov.: 33 AF XY: 0.0876 AC XY: 6517 AN XY: 74374

Gnomad4 AFR AF: 0.0790

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0156

Gnomad4 NFE AF: 0.0511

Gnomad4 OTH AF: 0.0876

Alfa AF: 0.0657 Hom.: 65

Bravo AF: 0.0969

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.45

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: rs829837; hg19: chr12-26121730;