chr7-66565625-T-C

Position:

• chr7-66565625-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_111972.1(RABGEF1P1):​n.496-4950A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0040 (0 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: RABGEF1P1 NR_111972.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

RABGEF1P1 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RABGEF1P1	NR_111972.1	n.496-4950A>G		intron_variant
RABGEF1P1	NR_111973.1	n.509-4950A>G		intron_variant
RABGEF1P1	NR_111974.1	n.317+7760A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RABGEF1P1	ENST00000428370.1	n.329+7764A>G		intron_variant		6
ENSG00000291136	ENST00000638711.1	n.750+7760A>G		intron_variant		5
ENSG00000291136	ENST00000639011.1	n.296+7760A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 562 AN: 139376 Hom.: 0 Cov.: 31 FAILED QC

Gnomad AFR AF: 0.00178

Gnomad AMI AF: 0.00120

Gnomad AMR AF: 0.00448

Gnomad ASJ AF: 0.00812

Gnomad EAS AF: 0.00899

Gnomad SAS AF: 0.00478

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00295

Gnomad OTH AF: 0.00472

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00403 AC: 562 AN: 139492 Hom.: 0 Cov.: 31 AF XY: 0.00485 AC XY: 330 AN XY: 68060

Gnomad4 AFR AF: 0.00177

Gnomad4 AMR AF: 0.00448

Gnomad4 ASJ AF: 0.00812

Gnomad4 EAS AF: 0.00902

Gnomad4 SAS AF: 0.00478

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.00295

Gnomad4 OTH AF: 0.00468

Alfa AF: 0.00127 Hom.: 18446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.90
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs801193; hg19: chr7-66030612;