rs1033180

Variant names:

• chr6-383546-C-T
• rs1033180
• ENST00000793853.1:n.394+3435G>A

Variant summary

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

The ENST00000793853.1(ENSG00000303358):​n.394+3435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 152,186 control chromosomes in the GnomAD database, including 297 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 0.053 (297 hom., cov: 33)
• Consequence: ENSG00000303358 ENST00000793853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 31 publications found

Genes affected

ENSG00000303358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0733 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
ENSG00000303358	ENST00000793853.1	n.394+3435G>A		intron_variant	Intron 1 of 1
ENSG00000303358	ENST00000793854.1	n.263+3435G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0529 AC: 8039 AN: 152068 Hom.: 297 Cov.: 33

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0465

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0528 AC: 8036 AN: 152186 Hom.: 297 Cov.: 33 AF XY: 0.0540 AC XY: 4021 AN XY: 74414

African (AFR) AF: 0.0126 AC: 524 AN: 41518

American (AMR) AF: 0.0464 AC: 710 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00829 AC: 40 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10588

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0751 AC: 5103 AN: 67984

Other (OTH) AF: 0.0539 AC: 114 AN: 2114

Alfa AF: 0.0629 Hom.: 1125

Bravo AF: 0.0454

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1033180; hg19: chr6-383546;