chr10-44398416-A-G

Variant names:

• chr10-44398416-A-G
• rs1023262
• ENST00000791650.1:n.172+139A>G

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.172+139A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,190 control chromosomes in the GnomAD database, including 37,906 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 0.68 (37906 hom., cov: 34)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303087	ENST00000791650.1		n.172+139A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103606 AN: 152072 Hom.: 37896 Cov.: 34

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.681 AC: 103648 AN: 152190 Hom.: 37906 Cov.: 34 AF XY: 0.687 AC XY: 51130 AN XY: 74418

African (AFR) AF: 0.386 AC: 16031 AN: 41504

American (AMR) AF: 0.779 AC: 11919 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2638 AN: 3468

East Asian (EAS) AF: 0.869 AC: 4485 AN: 5162

South Asian (SAS) AF: 0.764 AC: 3687 AN: 4824

European-Finnish (FIN) AF: 0.822 AC: 8718 AN: 10612

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.789 AC: 53664 AN: 68006

Other (OTH) AF: 0.725 AC: 1534 AN: 2116

Alfa AF: 0.750 Hom.: 37172

Bravo AF: 0.667

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs1023262; hg19: chr10-44893864;