rs4293143

Variant names:

• chr11-83110340-T-G
• rs4293143
• ENST00000752748.1:n.1658A>C

Variant summary

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

The ENST00000752748.1(ENSG00000298055):​n.1658A>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 0.23 in 152,242 control chromosomes in the GnomAD database, including 4,539 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 0.23 (4539 hom., cov: 33)
• Consequence: ENSG00000298055 ENST00000752748.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 11 publications found

Genes affected

ENSG00000298055 (HGNC:):

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=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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
ENSG00000298055	ENST00000752748.1	n.1658A>C		non_coding_transcript_exon_variant	Exon 3 of 3
RAB30-DT	ENST00000752551.1	n.144+37638T>G		intron_variant	Intron 2 of 2
RAB30-DT	ENST00000752552.1	n.210+3309T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34947 AN: 152124 Hom.: 4538 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.230 AC: 34961 AN: 152242 Hom.: 4539 Cov.: 33 AF XY: 0.228 AC XY: 16934 AN XY: 74428

African (AFR) AF: 0.110 AC: 4585 AN: 41562

American (AMR) AF: 0.235 AC: 3590 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1049 AN: 5172

South Asian (SAS) AF: 0.169 AC: 813 AN: 4824

European-Finnish (FIN) AF: 0.277 AC: 2936 AN: 10602

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20155 AN: 68000

Other (OTH) AF: 0.220 AC: 465 AN: 2116

Alfa AF: 0.273 Hom.: 14471

Bravo AF: 0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.89
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4293143; hg19: chr11-82821382;