rs10824815

Variant names:

• chr10-52840206-A-G
• rs10824815
• ENST00000816733.1:n.693-16534A>G

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.693-16534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,908 control chromosomes in the GnomAD database, including 4,658 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 0.24 (4658 hom., cov: 31)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 2 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816733.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306279	ENST00000816733.1		n.693-16534A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37071 AN: 151790 Hom.: 4649 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.244 AC: 37098 AN: 151908 Hom.: 4658 Cov.: 31 AF XY: 0.244 AC XY: 18148 AN XY: 74252

African (AFR) AF: 0.240 AC: 9959 AN: 41438

American (AMR) AF: 0.333 AC: 5075 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3472

East Asian (EAS) AF: 0.299 AC: 1532 AN: 5122

South Asian (SAS) AF: 0.225 AC: 1083 AN: 4818

European-Finnish (FIN) AF: 0.199 AC: 2099 AN: 10572

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15931 AN: 67942

Other (OTH) AF: 0.249 AC: 524 AN: 2108

Alfa AF: 0.242 Hom.: 566

Bravo AF: 0.256

Asia WGS AF: 0.249 AC: 865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10824815; hg19: chr10-54599966;