7-66565625-T-C

Variant names:

• chr7-66565625-T-C
• rs801193
• ENST00000428370.1:n.329+7764A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000428370.1(RABGEF1P1):​n.329+7764A>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 ENST00000428370.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 19 publications found

Genes affected

RABGEF1P1 (HGNC:55751): (RABGEF1 pseudogene 1)

RABGEF1P1 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RABGEF1P1	NR_111972.1	n.496-4950A>G		intron_variant	Intron 3 of 4
RABGEF1P1	NR_111973.1	n.509-4950A>G		intron_variant	Intron 4 of 10
RABGEF1P1	NR_111974.1	n.317+7760A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RABGEF1P1	ENST00000428370.1	n.329+7764A>G		intron_variant	Intron 2 of 2	6
RABGEF1P1	ENST00000638711.2	n.750+7760A>G		intron_variant	Intron 5 of 5	5
RABGEF1P1	ENST00000639011.2	n.298+7760A>G		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.00403 AC: 562 AN: 139376 Hom.: 0 Cov.: 31

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00177 AC: 71 AN: 40062

American (AMR) AF: 0.00448 AC: 63 AN: 14072

Ashkenazi Jewish (ASJ) AF: 0.00812 AC: 24 AN: 2956

East Asian (EAS) AF: 0.00902 AC: 37 AN: 4104

South Asian (SAS) AF: 0.00478 AC: 21 AN: 4392

European-Finnish (FIN) AF: 0.0174 AC: 153 AN: 8810

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 256

European-Non Finnish (NFE) AF: 0.00295 AC: 183 AN: 62086

Other (OTH) AF: 0.00468 AC: 9 AN: 1922

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000754 Hom.: 34223

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs801193; hg19: chr7-66030612;