7-66586918-T-C

Position:

• chr7-66586918-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_111973.1(RABGEF1P1):​n.220+1594A>G variant causes a intron, non coding transcript 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 NR_111973.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
RABGEF1P1	NR_111973.1	n.220+1594A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000692299.1	n.141+5339A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0605

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0521 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1267819; hg19: chr7-66051905;