rs11003193

Variant names:

• chr10-52830639-C-T
• rs11003193
• ENST00000816733.1:n.692+19942C>T

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+19942C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,844 control chromosomes in the GnomAD database, including 17,543 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 0.45 (17543 hom., cov: 32)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 3 publications found

Genes affected

ENSG00000306279 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.568 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
ENSG00000306279	ENST00000816733.1	n.692+19942C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67962 AN: 151726 Hom.: 17541 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.448 AC: 67964 AN: 151844 Hom.: 17543 Cov.: 32 AF XY: 0.448 AC XY: 33278 AN XY: 74208

African (AFR) AF: 0.190 AC: 7863 AN: 41430

American (AMR) AF: 0.382 AC: 5827 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1961 AN: 3466

East Asian (EAS) AF: 0.529 AC: 2730 AN: 5160

South Asian (SAS) AF: 0.536 AC: 2585 AN: 4824

European-Finnish (FIN) AF: 0.611 AC: 6444 AN: 10554

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38868 AN: 67862

Other (OTH) AF: 0.465 AC: 981 AN: 2108

Alfa AF: 0.517 Hom.: 21722

Bravo AF: 0.418

Asia WGS AF: 0.537 AC: 1868 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	0.74
DANN	Benign	0.81
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11003193; hg19: chr10-54590399;