19-48721227-C-T

Variant names:

• chr19-48721227-C-T
• rs281393
• NM_017805.3:c.2693-230G>A

Variant summary

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

The NM_017805.3(RASIP1):​c.2693-230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,844 control chromosomes in the GnomAD database, including 12,065 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.39 (12065 hom., cov: 30)
• Consequence: RASIP1 NM_017805.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.36
• Publications: 16 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017805.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RASIP1	NM_017805.3	MANE Select	c.2693-230G>A		intron	N/A	NP_060275.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RASIP1	ENST00000222145.9	TSL:1 MANE Select	c.2693-230G>A		intron	N/A	ENSP00000222145.3
	RASIP1	ENST00000963671.1		c.2699-200G>A		intron	N/A	ENSP00000633730.1
	RASIP1	ENST00000862294.1		c.2693-200G>A		intron	N/A	ENSP00000532353.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58625 AN: 151726 Hom.: 12068 Cov.: 30

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.386 AC: 58657 AN: 151844 Hom.: 12065 Cov.: 30 AF XY: 0.392 AC XY: 29047 AN XY: 74186

African (AFR) AF: 0.355 AC: 14698 AN: 41386

American (AMR) AF: 0.456 AC: 6961 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4251 AN: 5146

South Asian (SAS) AF: 0.427 AC: 2049 AN: 4796

European-Finnish (FIN) AF: 0.395 AC: 4170 AN: 10548

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.350 AC: 23791 AN: 67926

Other (OTH) AF: 0.390 AC: 822 AN: 2108

Alfa AF: 0.368 Hom.: 35743

Bravo AF: 0.394

Asia WGS AF: 0.636 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.035
DANN	Benign	0.74
PhyloP100		-4.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs281393; hg19: chr19-49224484;