11-58806534-A-G

Variant names:

• chr11-58806534-A-G
• rs10501373
• ENST00000529451.2:n.423+35699A>G

Variant summary

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

The ENST00000529451.2(ENSG00000289621):​n.423+35699A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 151,974 control chromosomes in the GnomAD database, including 189 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 0.034 (189 hom., cov: 32)
• Consequence: ENSG00000289621 ENST00000529451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893
• Publications: 2 publications found

Genes affected

ENSG00000289621 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529451.2. 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
	ENSG00000289621	ENST00000529451.2	TSL:2	n.423+35699A>G		intron	N/A
	ENSG00000289621	ENST00000766632.1		n.421+35699A>G		intron	N/A
	ENSG00000289621	ENST00000766633.1		n.459+35699A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0336 AC: 5104 AN: 151856 Hom.: 187 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0331

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

GnomAD4 genome AF: 0.0337 AC: 5115 AN: 151974 Hom.: 189 Cov.: 32 AF XY: 0.0366 AC XY: 2720 AN XY: 74276

African (AFR) AF: 0.0267 AC: 1109 AN: 41512

American (AMR) AF: 0.0446 AC: 678 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3462

East Asian (EAS) AF: 0.208 AC: 1073 AN: 5150

South Asian (SAS) AF: 0.106 AC: 513 AN: 4818

European-Finnish (FIN) AF: 0.0242 AC: 257 AN: 10602

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1325 AN: 67910

Other (OTH) AF: 0.0327 AC: 69 AN: 2108

Alfa AF: 0.0103 Hom.: 1

Bravo AF: 0.0360

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.85
PhyloP100		0.89

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: rs10501373;

hg19: chr11-58574007;