rs7846911

Variant names:

• chr9-83152514-C-T
• rs7846911
• ENST00000798701.1:n.322-34255G>A

Variant summary

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

The ENST00000798701.1(ENSG00000303992):​n.322-34255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,132 control chromosomes in the GnomAD database, including 2,319 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 0.17 (2319 hom., cov: 32)
• Consequence: ENSG00000303992 ENST00000798701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628
• Publications: 2 publications found

Genes affected

ENSG00000303992 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASEF	XM_047422827.1	c.-119+66368G>A		intron_variant	Intron 2 of 17		XP_047278783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303992	ENST00000798701.1	n.322-34255G>A		intron_variant	Intron 3 of 5
ENSG00000303992	ENST00000798702.1	n.328-34255G>A		intron_variant	Intron 1 of 3
ENSG00000303992	ENST00000798703.1	n.193-34255G>A		intron_variant	Intron 2 of 4
ENSG00000303992	ENST00000798704.1	n.186-34255G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25396 AN: 152014 Hom.: 2311 Cov.: 32

Gnomad AFR AF: 0.0928

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.167 AC: 25433 AN: 152132 Hom.: 2319 Cov.: 32 AF XY: 0.165 AC XY: 12255 AN XY: 74360

African (AFR) AF: 0.0930 AC: 3862 AN: 41520

American (AMR) AF: 0.200 AC: 3058 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3464

East Asian (EAS) AF: 0.144 AC: 743 AN: 5166

South Asian (SAS) AF: 0.189 AC: 914 AN: 4826

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14008 AN: 67978

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.183 Hom.: 607

Bravo AF: 0.171

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.33
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7846911; hg19: chr9-85767429;