rs7252574

Positions:

• chr19-8376895-C-T

Variant summary

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

The ENST00000593581.6(RAB11B-AS1):​n.783+67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,110 control chromosomes in the GnomAD database, including 18,673 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 0.49 (18644 hom., cov: 30)
  • Exomes 𝑓: 0.47 (29 hom.)
• Consequence: RAB11B-AS1 ENST00000593581.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

Genes affected

RAB11B-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAB11B-AS1	NR_038237.1	n.789+67G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB11B-AS1	ENST00000593581.6	n.783+67G>A		intron_variant		1
RAB11B-AS1	ENST00000597407.1	n.186+67G>A		intron_variant		3
RAB11B-AS1	ENST00000597785.1	n.279+10G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74012 AN: 151718 Hom.: 18636 Cov.: 30

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.0819

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.474 AC: 130 AN: 274 Hom.: 29 Cov.: 0 AF XY: 0.505 AC XY: 93 AN XY: 184

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.625

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.491

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.488 AC: 74070 AN: 151836 Hom.: 18644 Cov.: 30 AF XY: 0.486 AC XY: 36030 AN XY: 74182

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.0825

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.501

Alfa AF: 0.512 Hom.: 2462

Bravo AF: 0.481

Asia WGS AF: 0.348 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7252574; hg19: chr19-8441779; COSMIC: COSV56845707;