rs1808536

Variant names:

• chr19-8376973-A-G
• rs1808536
• ENST00000593581.7:n.772T>C

Variant summary

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

The ENST00000593581.7(RAB11B-AS1):​n.772T>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 ENST00000593581.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RAB11B-AS1	NR_038237.1	n.778T>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11B-AS1	ENST00000593581.7	n.772T>C		non_coding_transcript_exon_variant	Exon 2 of 3	1
RAB11B-AS1	ENST00000597407.1	n.175T>C		non_coding_transcript_exon_variant	Exon 2 of 3	3
RAB11B-AS1	ENST00000597785.1	n.211T>C		non_coding_transcript_exon_variant	Exon 2 of 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

African (AFR) AF: 0.417 AC: 5 AN: 12

American (AMR) AF: 0.500 AC: 4 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 6 AN: 8

East Asian (EAS) AF: 0.462 AC: 12 AN: 26

South Asian (SAS) AF: 0.875 AC: 14 AN: 16

European-Finnish (FIN) AF: 0.800 AC: 8 AN: 10

Middle Eastern (MID) AF: 1.00 AC: 8 AN: 8

European-Non Finnish (NFE) AF: 0.771 AC: 327 AN: 424

Other (OTH) AF: 0.692 AC: 18 AN: 26

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

African (AFR) AF: 0.716 AC: 29669 AN: 41426

American (AMR) AF: 0.769 AC: 11743 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3110 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1808 AN: 5140

South Asian (SAS) AF: 0.683 AC: 3279 AN: 4804

European-Finnish (FIN) AF: 0.871 AC: 9197 AN: 10562

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55701 AN: 67974

Other (OTH) AF: 0.767 AC: 1619 AN: 2112

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
PhyloP100		-3.1

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

Other links and lift over

dbSNP: rs1808536; hg19: chr19-8441857;