10-93753053-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793614.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303320	ENST00000793614.1		n.208-3069G>A		intron	N/A
	ENSG00000303320	ENST00000793616.1		n.244-3069G>A		intron	N/A
	ENSG00000303320	ENST00000793617.1		n.757+2484G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs946553;

hg19: chr10-95512810;