NM_001394098.1:c.104-2868C>T

Variant names:

• chr12-26061630-C-T
• rs10505990
• NM_001394098.1:c.104-2868C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394098.1(RASSF8):​c.104-2868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0534 in 152,130 control chromosomes in the GnomAD database, including 659 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 0.053 (659 hom., cov: 33)
• Consequence: RASSF8 NM_001394098.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF8	NM_001394098.1	c.104-2868C>T		intron_variant	Intron 3 of 5	ENST00000689635.1	NP_001381027.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF8	ENST00000689635.1	c.104-2868C>T		intron_variant	Intron 3 of 5		NM_001394098.1	ENSP00000510086.1

Frequencies

GnomAD3 genomes AF: 0.0533 AC: 8103 AN: 152010 Hom.: 651 Cov.: 33

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0461

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.000378

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00381

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0534 AC: 8126 AN: 152130 Hom.: 659 Cov.: 33 AF XY: 0.0587 AC XY: 4362 AN XY: 74358

African (AFR) AF: 0.0679 AC: 2820 AN: 41518

American (AMR) AF: 0.158 AC: 2407 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0461 AC: 160 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1505 AN: 5170

South Asian (SAS) AF: 0.176 AC: 845 AN: 4814

European-Finnish (FIN) AF: 0.000378 AC: 4 AN: 10576

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00381 AC: 259 AN: 67996

Other (OTH) AF: 0.0587 AC: 124 AN: 2112

Alfa AF: 0.0495 Hom.: 203

Bravo AF: 0.0649

Asia WGS AF: 0.219 AC: 757 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		0.023
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10505990; hg19: chr12-26214563;