10-58459892-G-A

Variant names:

• chr10-58459892-G-A
• rs1125139
• ENST00000720299.1:n.532+11056G>A

Variant summary

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

The ENST00000720299.1(ENSG00000293977):​n.532+11056G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,164 control chromosomes in the GnomAD database, including 48,388 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 0.80 (48388 hom., cov: 33)
• Consequence: ENSG00000293977 ENST00000720299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659
• Publications: 2 publications found

Genes affected

ENSG00000293977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378316	XR_007062374.1	n.96-7293G>A		intron_variant	Intron 1 of 3
LOC105378316	XR_945981.3	n.361-7293G>A		intron_variant	Intron 2 of 5
LOC105378316	XR_945982.3	n.361-7293G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293977	ENST00000720299.1	n.532+11056G>A		intron_variant	Intron 1 of 1
ENSG00000293977	ENST00000720300.1	n.97+5057G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.795 AC: 120928 AN: 152046 Hom.: 48337 Cov.: 33

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.795 AC: 121029 AN: 152164 Hom.: 48388 Cov.: 33 AF XY: 0.789 AC XY: 58706 AN XY: 74368

African (AFR) AF: 0.861 AC: 35755 AN: 41538

American (AMR) AF: 0.818 AC: 12500 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2511 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3571 AN: 5168

South Asian (SAS) AF: 0.586 AC: 2818 AN: 4812

European-Finnish (FIN) AF: 0.718 AC: 7593 AN: 10582

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53720 AN: 67994

Other (OTH) AF: 0.764 AC: 1614 AN: 2112

Alfa AF: 0.781 Hom.: 5763

Bravo AF: 0.811

Asia WGS AF: 0.617 AC: 2150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1125139; hg19: chr10-60219652;