rs10867921

chr9-82994866-G-Achr9-82994866-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152573.4(RASEF):c.1921-1841C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,110 control chromosomes in the GnomAD database, including 467 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 (467 hom., cov: 32)
• Consequence: RASEF NM_152573.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

Genes affected

RASEF (HGNC:26464): (RAS and EF-hand domain containing) This gene is a member of the Rab family of GTPases that are involved in regulation of membrane traffic. The encoded protein contains an N-terminal EF-hand domain, a coiled-coil motif and a C-terminal Rab domain. A potential role as tumor suppressor has been indicated for this gene. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RASEF	NM_152573.4	c.1921-1841C>T		intron_variant		ENST00000376447.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RASEF	ENST00000376447.4	c.1921-1841C>T		intron_variant		1	NM_152573.4	P1

Frequencies

GnomAD3 genomes AF: 0.0717 AC: 10895 AN: 151990 Hom.: 465 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0266

Gnomad SAS AF: 0.0525

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0671

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

GnomAD4 genome AF: 0.0716 AC: 10894 AN: 152110 Hom.: 467 Cov.: 32 AF XY: 0.0736 AC XY: 5472 AN XY: 74340

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0411

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0265

Gnomad4 SAS AF: 0.0519

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0644

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0580 Hom.: 438

Bravo AF: 0.0660

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	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

Publications

LitVar

Other links and lift over

dbSNP: rs10867921; hg19: chr9-85609781;