rs17400257

Variant names:

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

Variant summary

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

The XM_047422827.1(RASEF):​c.-119+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: RASEF XM_047422827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RASEF	XM_047422827.1	c.-119+20844G>T		intron_variant	Intron 2 of 17		XP_047278783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0207

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0988

Gnomad4 EAS AF: 0.0380

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.110

Alfa AF: 0.111 Hom.: 1445

Bravo AF: 0.0918

Asia WGS AF: 0.114 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17400257; hg19: chr9-85812953;