chr10-44387113-C-G

Variant names:

• chr10-44387113-C-G
• rs1413519
• ENST00000791650.1:n.51+2937C>G

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.51+2937C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,182 control chromosomes in the GnomAD database, including 46,934 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 0.78 (46934 hom., cov: 34)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 6 publications found

Genes affected

ENSG00000303087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791650.1. 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
	ENSG00000303087	ENST00000791650.1		n.51+2937C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118596 AN: 152064 Hom.: 46905 Cov.: 34

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.780 AC: 118675 AN: 152182 Hom.: 46934 Cov.: 34 AF XY: 0.786 AC XY: 58496 AN XY: 74438

African (AFR) AF: 0.628 AC: 26041 AN: 41490

American (AMR) AF: 0.870 AC: 13320 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2898 AN: 3472

East Asian (EAS) AF: 0.808 AC: 4157 AN: 5142

South Asian (SAS) AF: 0.787 AC: 3796 AN: 4822

European-Finnish (FIN) AF: 0.908 AC: 9656 AN: 10630

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56118 AN: 68006

Other (OTH) AF: 0.824 AC: 1742 AN: 2114

Alfa AF: 0.801 Hom.: 6113

Bravo AF: 0.772

Asia WGS AF: 0.772 AC: 2682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.3
DANN	Benign	0.76
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1413519; hg19: chr10-44882561;