rs12569261

Variant names:

• chr1-206553932-A-G
• rs12569261
• NM_182663.4:c.579+15639A>G

Variant summary

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

The NM_182663.4(RASSF5):​c.579+15639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,182 control chromosomes in the GnomAD database, including 3,438 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 0.20 (3438 hom., cov: 33)
• Consequence: RASSF5 NM_182663.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 13 publications found

Genes affected

RASSF5 (HGNC:17609): (Ras association domain family member 5) This gene is a member of the Ras association domain family. It functions as a tumor suppressor, and is inactivated in a variety of cancers. The encoded protein localizes to centrosomes and microtubules, and associates with the GTP-activated forms of Ras, Rap1, and several other Ras-like small GTPases. The protein regulates lymphocyte adhesion and suppresses cell growth in response to activated Rap1 or Ras. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF5	NM_182663.4	c.579+15639A>G		intron_variant	Intron 2 of 5	ENST00000579436.7	NP_872604.1
RASSF5	NM_182664.4	c.579+15639A>G		intron_variant	Intron 2 of 4		NP_872605.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF5	ENST00000579436.7	c.579+15639A>G		intron_variant	Intron 2 of 5	1	NM_182663.4	ENSP00000462099.1
RASSF5	ENST00000581503.6	c.579+15639A>G		intron_variant	Intron 2 of 3	1		ENSP00000464039.2
RASSF5	ENST00000580449.5	c.579+15639A>G		intron_variant	Intron 2 of 4	1		ENSP00000462544.1
RASSF5	ENST00000636182.1	c.279+15639A>G		intron_variant	Intron 2 of 5	5		ENSP00000489689.1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31081 AN: 152064 Hom.: 3439 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.204 AC: 31086 AN: 152182 Hom.: 3438 Cov.: 33 AF XY: 0.208 AC XY: 15469 AN XY: 74392

African (AFR) AF: 0.118 AC: 4889 AN: 41520

American (AMR) AF: 0.257 AC: 3936 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1143 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1316 AN: 5188

South Asian (SAS) AF: 0.236 AC: 1138 AN: 4828

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10584

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15676 AN: 67986

Other (OTH) AF: 0.231 AC: 487 AN: 2108

Alfa AF: 0.228 Hom.: 17530

Bravo AF: 0.204

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.6
DANN	Benign	0.68
PhyloP100		0.53

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: rs12569261; hg19: chr1-206727260;