10-44392682-A-G

Variant names:

• chr10-44392682-A-G
• rs6593412
• ENST00000791650.1:n.52-5475A>G

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.52-5475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,910 control chromosomes in the GnomAD database, including 22,328 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 0.53 (22328 hom., cov: 31)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.633 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.52-5475A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79864 AN: 151792 Hom.: 22328 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.526 AC: 79882 AN: 151910 Hom.: 22328 Cov.: 31 AF XY: 0.528 AC XY: 39228 AN XY: 74238

African (AFR) AF: 0.362 AC: 14993 AN: 41406

American (AMR) AF: 0.644 AC: 9838 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1944 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5162

South Asian (SAS) AF: 0.436 AC: 2090 AN: 4792

European-Finnish (FIN) AF: 0.668 AC: 7046 AN: 10542

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.603 AC: 40954 AN: 67950

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.574 Hom.: 68101

Bravo AF: 0.519

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6593412;

hg19: chr10-44888130;