rs946553

Variant names:

• chr10-93753053-C-T
• rs946553
• ENST00000793614.1:n.208-3069G>A

Variant summary

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

The ENST00000793614.1(ENSG00000303320):​n.208-3069G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,048 control chromosomes in the GnomAD database, including 29,101 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 0.61 (29101 hom., cov: 32)
• Consequence: ENSG00000303320 ENST00000793614.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 5 publications found

Genes affected

ENSG00000303320 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927013	XR_246160.5	n.238-3069G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303320	ENST00000793614.1	n.208-3069G>A		intron_variant	Intron 1 of 3
ENSG00000303320	ENST00000793616.1	n.244-3069G>A		intron_variant	Intron 1 of 2
ENSG00000303320	ENST00000793617.1	n.757+2484G>A		intron_variant	Intron 2 of 2
ENSG00000303320	ENST00000793618.1	n.618+4428G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93321 AN: 151930 Hom.: 29090 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.614 AC: 93367 AN: 152048 Hom.: 29101 Cov.: 32 AF XY: 0.619 AC XY: 46009 AN XY: 74356

African (AFR) AF: 0.519 AC: 21519 AN: 41438

American (AMR) AF: 0.596 AC: 9113 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2314 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4325 AN: 5182

South Asian (SAS) AF: 0.707 AC: 3410 AN: 4822

European-Finnish (FIN) AF: 0.663 AC: 7007 AN: 10568

Middle Eastern (MID) AF: 0.710 AC: 206 AN: 290

European-Non Finnish (NFE) AF: 0.642 AC: 43619 AN: 67968

Other (OTH) AF: 0.605 AC: 1279 AN: 2114

Alfa AF: 0.631 Hom.: 46303

Bravo AF: 0.608

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
DANN	Benign	0.32
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs946553; hg19: chr10-95512810;