rs10994143

Variant names:

• chr10-60021320-A-G
• rs10994143
• ENST00000830353.1:n.83-29233A>G

Variant summary

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

The ENST00000830353.1(ENSG00000232682):​n.83-29233A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0493 in 152,310 control chromosomes in the GnomAD database, including 427 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 0.049 (427 hom., cov: 33)
• Consequence: ENSG00000232682 ENST00000830353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 1 publications found

Genes affected

ENSG00000232682 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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
ENSG00000232682	ENST00000830353.1	n.83-29233A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0492 AC: 7488 AN: 152192 Hom.: 427 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0368

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

GnomAD4 genome AF: 0.0493 AC: 7502 AN: 152310 Hom.: 427 Cov.: 33 AF XY: 0.0472 AC XY: 3515 AN XY: 74486

African (AFR) AF: 0.143 AC: 5926 AN: 41560

American (AMR) AF: 0.0147 AC: 225 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.00230 AC: 8 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.00331 AC: 16 AN: 4828

European-Finnish (FIN) AF: 0.0162 AC: 172 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1068 AN: 68024

Other (OTH) AF: 0.0360 AC: 76 AN: 2114

Alfa AF: 0.0446 Hom.: 47

Bravo AF: 0.0521

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.70
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10994143; hg19: chr10-61781078;