rs281408

Variant names:

• chr19-48730149-C-A
• rs281408
• NM_017805.3:c.1180-559G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-48730149-C-A
• chr19-48730149-C-G
• chr19-48730149-C-T

Variant summary

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

The NM_017805.3(RASIP1):​c.1180-559G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,444 control chromosomes in the GnomAD database, including 14,326 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 0.42 (14326 hom., cov: 28)
• Consequence: RASIP1 NM_017805.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 32 publications found

Genes affected

RASIP1 (HGNC:24716): (Ras interacting protein 1) Enables GTPase binding activity and protein homodimerization activity. Involved in several processes, including negative regulation of Rho protein signal transduction; negative regulation of Rho-dependent protein serine/threonine kinase activity; and positive regulation of integrin activation. Located in cell-cell junction. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

LOC124904737 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASIP1	NM_017805.3	c.1180-559G>T		intron_variant	Intron 4 of 11	ENST00000222145.9	NP_060275.2
LOC124904737	XR_007067286.1	n.226-1117C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASIP1	ENST00000222145.9	c.1180-559G>T		intron_variant	Intron 4 of 11	1	NM_017805.3	ENSP00000222145.3
RASIP1	ENST00000599291.1	c.414+5047G>T		intron_variant	Intron 2 of 2	3		ENSP00000471633.1
RASIP1	ENST00000594232.1	n.577-559G>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.422 AC: 63815 AN: 151326 Hom.: 14333 Cov.: 28

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.421 AC: 63830 AN: 151444 Hom.: 14326 Cov.: 28 AF XY: 0.425 AC XY: 31458 AN XY: 73966

African (AFR) AF: 0.305 AC: 12591 AN: 41266

American (AMR) AF: 0.496 AC: 7549 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1673 AN: 3466

East Asian (EAS) AF: 0.834 AC: 4262 AN: 5110

South Asian (SAS) AF: 0.489 AC: 2339 AN: 4788

European-Finnish (FIN) AF: 0.441 AC: 4613 AN: 10464

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29353 AN: 67834

Other (OTH) AF: 0.427 AC: 897 AN: 2100

Alfa AF: 0.439 Hom.: 33572

Bravo AF: 0.423

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.75
PhyloP100		0.27
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: rs281408; hg19: chr19-49233406;