7-66586918-T-C

Variant names:

• chr7-66586918-T-C
• rs1267819
• ENST00000638711.2:n.210+1594A>G

Variant summary

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

The ENST00000638711.2(RABGEF1P1):​n.210+1594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,214 control chromosomes in the GnomAD database, including 982 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 0.10 (982 hom., cov: 32)
• Consequence: RABGEF1P1 ENST00000638711.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 6 publications found

Genes affected

RABGEF1P1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RABGEF1P1	NR_111972.1	n.151+5339A>G		intron_variant	Intron 1 of 4
RABGEF1P1	NR_111973.1	n.220+1594A>G		intron_variant	Intron 2 of 10
RABGEF1P1	NR_111974.1	n.151+5339A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RABGEF1P1	ENST00000638711.2	n.210+1594A>G		intron_variant	Intron 2 of 5	5
RABGEF1P1	ENST00000639011.2	n.132+5339A>G		intron_variant	Intron 1 of 5	5
RABGEF1P1	ENST00000639153.3	n.213+1594A>G		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15691 AN: 152096 Hom.: 979 Cov.: 32

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.103 AC: 15699 AN: 152214 Hom.: 982 Cov.: 32 AF XY: 0.105 AC XY: 7790 AN XY: 74408

African (AFR) AF: 0.0605 AC: 2511 AN: 41538

American (AMR) AF: 0.166 AC: 2531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3472

East Asian (EAS) AF: 0.143 AC: 744 AN: 5186

South Asian (SAS) AF: 0.198 AC: 952 AN: 4814

European-Finnish (FIN) AF: 0.0493 AC: 523 AN: 10612

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7311 AN: 67996

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.0526 Hom.: 52

Bravo AF: 0.111

Asia WGS AF: 0.148 AC: 520 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	3.9
DANN	Benign	0.67
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1267819; hg19: chr7-66051905;