rs10867921

Variant names:

• chr9-82994866-G-A
• rs10867921
• NM_152573.4:c.1921-1841C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-82994866-G-A
• chr9-82994866-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RASEF	NM_152573.4	c.1921-1841C>T		intron_variant	Intron 14 of 16	ENST00000376447.4	NP_689786.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RASEF	ENST00000376447.4	c.1921-1841C>T		intron_variant	Intron 14 of 16	1	NM_152573.4	ENSP00000365630.3

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

African (AFR) AF: 0.0926 AC: 3842 AN: 41494

American (AMR) AF: 0.0411 AC: 628 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.0265 AC: 137 AN: 5174

South Asian (SAS) AF: 0.0519 AC: 250 AN: 4816

European-Finnish (FIN) AF: 0.116 AC: 1220 AN: 10554

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4380 AN: 68006

Other (OTH) AF: 0.0682 AC: 144 AN: 2110

Alfa AF: 0.0613 Hom.: 1024

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
PhyloP100		0.23
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: rs10867921; hg19: chr9-85609781;