11-83098558-A-T

Position:

• chr11-83098558-A-T

Variant summary

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

The ENST00000658004.1(RAB30-DT):​n.409-7921A>T variant causes a intron, non coding transcript 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 ENST00000658004.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAB30-DT	ENST00000658004.1	n.409-7921A>T		intron_variant, non_coding_transcript_variant
RAB30-DT	ENST00000527627.5	n.264-7921A>T		intron_variant, non_coding_transcript_variant		3
RAB30-DT	ENST00000665456.1	n.106-7921A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.362

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7127866; hg19: chr11-82809600;