9-83152514-C-T

Variant names:

• chr9-83152514-C-T
• rs7846911
• XM_047422827.1:c.-119+66368G>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

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]

ENSG00000303992 (HGNC:):

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798701.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303992	ENST00000798701.1		n.322-34255G>A		intron	N/A
	ENSG00000303992	ENST00000798702.1		n.328-34255G>A		intron	N/A
	ENSG00000303992	ENST00000798703.1		n.193-34255G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7846911;

hg19: chr9-85767429;