rs7252574

Variant names:

• chr19-8376895-C-T
• rs7252574
• ENST00000593581.7:n.783+67G>A

Variant summary

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

The ENST00000593581.7(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 ENST00000593581.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 8 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=-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 rank	MANE	Protein	UniProt
RAB11B-AS1	NR_038237.1	n.789+67G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB11B-AS1	ENST00000593581.7	n.783+67G>A		intron_variant	Intron 2 of 2	1
RAB11B-AS1	ENST00000597407.1	n.186+67G>A		intron_variant	Intron 2 of 2	3
RAB11B-AS1	ENST00000597785.1	n.279+10G>A		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.375 AC: 3 AN: 8

American (AMR) AF: 0.625 AC: 5 AN: 8

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.600 AC: 6 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.491 AC: 108 AN: 220

Other (OTH) AF: 0.375 AC: 6 AN: 16

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

African (AFR) AF: 0.468 AC: 19385 AN: 41382

American (AMR) AF: 0.468 AC: 7128 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2054 AN: 3470

East Asian (EAS) AF: 0.0825 AC: 426 AN: 5166

South Asian (SAS) AF: 0.493 AC: 2369 AN: 4808

European-Finnish (FIN) AF: 0.519 AC: 5464 AN: 10520

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35639 AN: 67926

Other (OTH) AF: 0.501 AC: 1060 AN: 2116

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
PhyloP100		0.12

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

Other links and lift over

dbSNP: rs7252574; hg19: chr19-8441779; COSMIC: COSV56845707;