7-66565625-T-G

Variant names:

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

Variant summary

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

The ENST00000428370.1(RABGEF1P1):​n.329+7764A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 148,222 control chromosomes in the GnomAD database, including 20,412 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 0.52 (20412 hom., cov: 31)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.518 AC: 76741 AN: 148104 Hom.: 20383 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.518 AC: 76817 AN: 148222 Hom.: 20412 Cov.: 31 AF XY: 0.512 AC XY: 37072 AN XY: 72352

African (AFR) AF: 0.666 AC: 27305 AN: 40982

American (AMR) AF: 0.498 AC: 7387 AN: 14844

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1310 AN: 3328

East Asian (EAS) AF: 0.277 AC: 1342 AN: 4852

South Asian (SAS) AF: 0.368 AC: 1723 AN: 4686

European-Finnish (FIN) AF: 0.419 AC: 4186 AN: 9986

Middle Eastern (MID) AF: 0.365 AC: 100 AN: 274

European-Non Finnish (NFE) AF: 0.484 AC: 32118 AN: 66336

Other (OTH) AF: 0.491 AC: 1008 AN: 2054

Alfa AF: 0.477 Hom.: 34223

Bravo AF: 0.518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.54
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;