NM_182663.4:c.458-13256G>A

Variant names:

• chr1-206524916-G-A
• rs11118968
• NM_182663.4:c.458-13256G>A

Variant summary

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

The NM_182663.4(RASSF5):​c.458-13256G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.072 in 151,092 control chromosomes in the GnomAD database, including 663 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 0.072 (663 hom., cov: 28)
• Consequence: RASSF5 NM_182663.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASSF5	NM_182663.4	c.458-13256G>A		intron_variant	Intron 1 of 5	ENST00000579436.7	NP_872604.1
RASSF5	NM_182664.4	c.458-13256G>A		intron_variant	Intron 1 of 4		NP_872605.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASSF5	ENST00000579436.7	c.458-13256G>A		intron_variant	Intron 1 of 5	1	NM_182663.4	ENSP00000462099.1
RASSF5	ENST00000581503.6	c.458-13256G>A		intron_variant	Intron 1 of 3	1		ENSP00000464039.2
RASSF5	ENST00000580449.5	c.458-13256G>A		intron_variant	Intron 1 of 4	1		ENSP00000462544.1
RASSF5	ENST00000636182.1	c.157+6372G>A		intron_variant	Intron 1 of 5	5		ENSP00000489689.1

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10866 AN: 150976 Hom.: 665 Cov.: 28

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0442

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0606

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

GnomAD4 genome AF: 0.0720 AC: 10875 AN: 151092 Hom.: 663 Cov.: 28 AF XY: 0.0698 AC XY: 5153 AN XY: 73818

African (AFR) AF: 0.170 AC: 6990 AN: 41086

American (AMR) AF: 0.0461 AC: 696 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.0442 AC: 153 AN: 3464

East Asian (EAS) AF: 0.00408 AC: 21 AN: 5152

South Asian (SAS) AF: 0.0287 AC: 138 AN: 4802

European-Finnish (FIN) AF: 0.0376 AC: 390 AN: 10382

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0347 AC: 2355 AN: 67828

Other (OTH) AF: 0.0585 AC: 122 AN: 2086

Alfa AF: 0.0463 Hom.: 288

Bravo AF: 0.0765

Asia WGS AF: 0.0230 AC: 81 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.53
PhyloP100		0.80

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: rs11118968; hg19: chr1-206698249;