11-83098558-A-T

Variant names:

• chr11-83098558-A-T
• rs7127866
• ENST00000527627.5:n.264-7921A>T

Variant summary

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

The ENST00000527627.5(RAB30-DT):​n.264-7921A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,990 control chromosomes in the GnomAD database, including 14,911 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 0.39 (14911 hom., cov: 31)
• Consequence: RAB30-DT ENST00000527627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 5 publications found

Genes affected

RAB30-DT (HGNC:48672): (RAB30 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB30-DT	ENST00000527627.5	n.264-7921A>T		intron_variant	Intron 2 of 2	3
RAB30-DT	ENST00000658004.1	n.409-7921A>T		intron_variant	Intron 3 of 3
RAB30-DT	ENST00000665456.1	n.106-7921A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59194 AN: 151872 Hom.: 14879 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.363

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.390 AC: 59270 AN: 151990 Hom.: 14911 Cov.: 31 AF XY: 0.390 AC XY: 28942 AN XY: 74282

African (AFR) AF: 0.717 AC: 29723 AN: 41428

American (AMR) AF: 0.283 AC: 4320 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2125 AN: 5170

South Asian (SAS) AF: 0.461 AC: 2222 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2457 AN: 10564

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16411 AN: 67956

Other (OTH) AF: 0.362 AC: 764 AN: 2108

Alfa AF: 0.164 Hom.: 339

Bravo AF: 0.406

Asia WGS AF: 0.475 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.98
DANN	Benign	0.16
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs7127866; hg19: chr11-82809600;