rs17400257

Variant names:

• chr9-83198038-C-A
• rs17400257
• XM_047422827.1:c.-119+20844G>T

Variant summary

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

The ENST00000798701.1(ENSG00000303992):​n.321+20844G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,282 control chromosomes in the GnomAD database, including 908 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 0.095 (908 hom., cov: 32)
• Consequence: ENSG00000303992 ENST00000798701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.169 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.321+20844G>T		intron	N/A
	ENSG00000303992	ENST00000798702.1		n.327+20844G>T		intron	N/A
	ENSG00000303992	ENST00000798703.1		n.192+20844G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0945 AC: 14379 AN: 152164 Hom.: 903 Cov.: 32

Gnomad AFR AF: 0.0208

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0988

Gnomad EAS AF: 0.0383

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0945 AC: 14391 AN: 152282 Hom.: 908 Cov.: 32 AF XY: 0.0974 AC XY: 7252 AN XY: 74452

African (AFR) AF: 0.0207 AC: 860 AN: 41570

American (AMR) AF: 0.175 AC: 2677 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0988 AC: 343 AN: 3472

East Asian (EAS) AF: 0.0380 AC: 197 AN: 5180

South Asian (SAS) AF: 0.128 AC: 618 AN: 4830

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7505 AN: 68020

Other (OTH) AF: 0.110 AC: 232 AN: 2114

Alfa AF: 0.109 Hom.: 1784

Bravo AF: 0.0918

Asia WGS AF: 0.114 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.42
PhyloP100		0.22

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: rs17400257;

hg19: chr9-85812953;