rs41341649

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-229260325-C-A
• chr1-229260325-C-G

Variant summary

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

The NR_149312.1(RAB4A-AS1):​n.1854-1205G>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 NR_149312.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.618

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036773; hg19: chr1-229396072;