7-66565625-T-G

Position:

• chr7-66565625-T-G

Variant summary

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

The NR_111973.1(RABGEF1P1):​n.509-4950A>C 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 0.518 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 NR_111973.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
RABGEF1P1	NR_111973.1	n.509-4950A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RABGEF1P1	ENST00000428370.1	n.329+7764A>C		intron_variant, non_coding_transcript_variant
	ENST00000692299.1	n.307+7760A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.491

Alfa AF: 0.457 Hom.: 18446

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs801193; hg19: chr7-66030612;