rs1407127

Positions:

• chr1-174119548-T-C
• chr1-174119548-T-G

Variant summary

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

The ENST00000665650.1(RABGAP1L-DT):​n.520-3899A>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 0.229 in 152,150 control chromosomes in the GnomAD database, including 4,475 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 0.23 (4475 hom., cov: 32)
• Consequence: RABGAP1L-DT ENST00000665650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

Genes affected

RABGAP1L-DT (HGNC:54296): (RABGAP1L divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RABGAP1L-DT	ENST00000665650.1	n.520-3899A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34836 AN: 152032 Hom.: 4471 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0687

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.229 AC: 34852 AN: 152150 Hom.: 4475 Cov.: 32 AF XY: 0.230 AC XY: 17111 AN XY: 74376

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.0693

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.239

Alfa AF: 0.238 Hom.: 2387

Bravo AF: 0.223

Asia WGS AF: 0.198 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1407127; hg19: chr1-174088686;