1-229260325-C-A

Variant names:

• chr1-229260325-C-A
• rs2036773
• ENST00000429227.1:n.29-1205G>T

Variant summary

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

The ENST00000429227.1(RAB4A-AS1):​n.29-1205G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 151,124 control chromosomes in the GnomAD database, including 32,340 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 0.65 (32340 hom., cov: 29)
• Consequence: RAB4A-AS1 ENST00000429227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 0 publications found

Genes affected

RAB4A-AS1 (HGNC:55934): (RAB4A antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB4A-AS1	NR_149312.1	n.1854-1205G>T		intron_variant	Intron 2 of 2
RAB4A-AS1	NR_149313.1	n.180-1205G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB4A-AS1	ENST00000429227.1	n.29-1205G>T		intron_variant	Intron 1 of 1	5
RAB4A-AS1	ENST00000653511.1	n.1740-1205G>T		intron_variant	Intron 2 of 2
RAB4A-AS1	ENST00000654028.1	n.171-1205G>T		intron_variant	Intron 1 of 1
RAB4A-AS1	ENST00000656366.1	n.1447-1205G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.647 AC: 97710 AN: 151010 Hom.: 32299 Cov.: 29

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.647 AC: 97813 AN: 151124 Hom.: 32340 Cov.: 29 AF XY: 0.640 AC XY: 47181 AN XY: 73740

African (AFR) AF: 0.802 AC: 33033 AN: 41172

American (AMR) AF: 0.609 AC: 9247 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1772 AN: 3462

East Asian (EAS) AF: 0.518 AC: 2658 AN: 5134

South Asian (SAS) AF: 0.500 AC: 2395 AN: 4794

European-Finnish (FIN) AF: 0.584 AC: 6033 AN: 10336

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40765 AN: 67742

Other (OTH) AF: 0.618 AC: 1295 AN: 2096

Alfa AF: 0.492 Hom.: 1438

Bravo AF: 0.655

Asia WGS AF: 0.532 AC: 1849 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.23
PhyloP100		-2.3
Mutation Taster		=18/82	disease causing (long InDel)

Splicing

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

Other links and lift over

dbSNP: rs2036773; hg19: chr1-229396072;