rs10513821

Variant names:

• chr3-187825554-A-G
• rs10513821
• ENST00000793661.1:n.461+7870T>C

Variant summary

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

The ENST00000793661.1(ENSG00000303324):​n.461+7870T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,264 control chromosomes in the GnomAD database, including 1,371 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 0.12 (1371 hom., cov: 32)
• Consequence: ENSG00000303324 ENST00000793661.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 6 publications found

Genes affected

ENSG00000303324 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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
ENSG00000303324	ENST00000793661.1	n.461+7870T>C		intron_variant	Intron 3 of 6
ENSG00000303324	ENST00000793662.1	n.601-9484T>C		intron_variant	Intron 2 of 4
ENSG00000303324	ENST00000793663.1	n.617-32063T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18796 AN: 152146 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.0550

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.124 AC: 18806 AN: 152264 Hom.: 1371 Cov.: 32 AF XY: 0.123 AC XY: 9131 AN XY: 74450

African (AFR) AF: 0.0548 AC: 2279 AN: 41568

American (AMR) AF: 0.201 AC: 3069 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3466

East Asian (EAS) AF: 0.110 AC: 568 AN: 5182

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10610

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10188 AN: 68000

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.137 Hom.: 2123

Bravo AF: 0.128

Asia WGS AF: 0.0940 AC: 325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10513821; hg19: chr3-187543342;