chr7-66565625-T-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000428370.1(RABGEF1P1):​n.329+7764A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: RABGEF1P1 ENST00000428370.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 0 publications found

Genes affected

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

RABGEF1P1 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RABGEF1P1	NR_111972.1	n.496-4950A>T		intron_variant	Intron 3 of 4
RABGEF1P1	NR_111973.1	n.509-4950A>T		intron_variant	Intron 4 of 10
RABGEF1P1	NR_111974.1	n.317+7760A>T		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>T		intron_variant	Intron 2 of 2	6
RABGEF1P1	ENST00000638711.2	n.750+7760A>T		intron_variant	Intron 5 of 5	5
RABGEF1P1	ENST00000639011.2	n.298+7760A>T		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.56
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;