ENST00000419983.5:n.268+2536A>G

Variant names:

• chr1-174119548-T-C
• rs1407127
• ENST00000419983.5:n.268+2536A>G

Variant summary

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

The ENST00000419983.5(RABGAP1L-DT):​n.268+2536A>G variant causes a intron 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 ENST00000419983.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34
• Publications: 5 publications found

Genes affected

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

ENSG00000303090 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RABGAP1L-DT	ENST00000419983.5	n.268+2536A>G		intron_variant	Intron 3 of 3	3
RABGAP1L-DT	ENST00000426899.7	n.581-3899A>G		intron_variant	Intron 3 of 3	3
RABGAP1L-DT	ENST00000454467.5	n.319-3905A>G		intron_variant	Intron 2 of 2	5

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

African (AFR) AF: 0.145 AC: 6025 AN: 41520

American (AMR) AF: 0.267 AC: 4074 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1137 AN: 3472

East Asian (EAS) AF: 0.0693 AC: 359 AN: 5184

South Asian (SAS) AF: 0.250 AC: 1206 AN: 4828

European-Finnish (FIN) AF: 0.279 AC: 2957 AN: 10580

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18148 AN: 67974

Other (OTH) AF: 0.239 AC: 505 AN: 2110

Alfa AF: 0.242 Hom.: 2705

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1407127; hg19: chr1-174088686;