rs1808536

chr19-8376973-A-G

Variant summary

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

The NR_038237.1(RAB11B-AS1):n.778T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,498 control chromosomes in the GnomAD database, including 45,992 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 0.77 (45840 hom., cov: 30)
  • Exomes 𝑓: 0.75 (152 hom.)
• Consequence: RAB11B-AS1 NR_038237.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09

Genes affected

RAB11B-AS1 (HGNC:44178): (RAB11B antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAB11B-AS1	NR_038237.1	n.778T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAB11B-AS1	ENST00000593581.6	n.772T>C		non_coding_transcript_exon_variant	2/3	1
RAB11B-AS1	ENST00000597407.1	n.175T>C		non_coding_transcript_exon_variant	2/3	3
RAB11B-AS1	ENST00000597785.1	n.211T>C		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.770 AC: 116895 AN: 151842 Hom.: 45817 Cov.: 30

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.769

GnomAD4 exome AF: 0.747 AC: 402 AN: 538 Hom.: 152 Cov.: 0 AF XY: 0.766 AC XY: 314 AN XY: 410

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.462

Gnomad4 SAS exome AF: 0.875

Gnomad4 FIN exome AF: 0.800

Gnomad4 NFE exome AF: 0.771

Gnomad4 OTH exome AF: 0.692

GnomAD4 genome AF: 0.770 AC: 116977 AN: 151960 Hom.: 45840 Cov.: 30 AF XY: 0.770 AC XY: 57199 AN XY: 74262

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.769

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.767

Alfa AF: 0.809 Hom.: 6215

Bravo AF: 0.758

Asia WGS AF: 0.558 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.32
Dann	Benign	0.060

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1808536; hg19: chr19-8441857;