rs10520722

Variant names:

• chr15-93362604-T-A
• rs10520722
• ENST00000543286.5:n.545+40258T>A

Variant summary

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

The ENST00000543286.5(ENSG00000257060):​n.545+40258T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,982 control chromosomes in the GnomAD database, including 12,142 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 0.39 (12142 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000543286.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 0 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543286.5. 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
	ENSG00000257060	ENST00000543286.5	TSL:2	n.545+40258T>A		intron	N/A
	ENSG00000257060	ENST00000553478.1	TSL:4	n.318+40258T>A		intron	N/A
	ENSG00000257060	ENST00000554105.6	TSL:4	n.423-10906T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59542 AN: 151864 Hom.: 12131 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.392 AC: 59596 AN: 151982 Hom.: 12142 Cov.: 32 AF XY: 0.385 AC XY: 28591 AN XY: 74266

African (AFR) AF: 0.387 AC: 16043 AN: 41440

American (AMR) AF: 0.365 AC: 5577 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3470

East Asian (EAS) AF: 0.113 AC: 584 AN: 5178

South Asian (SAS) AF: 0.151 AC: 726 AN: 4820

European-Finnish (FIN) AF: 0.421 AC: 4432 AN: 10534

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29452 AN: 67948

Other (OTH) AF: 0.364 AC: 769 AN: 2112

Alfa AF: 0.421 Hom.: 1684

Bravo AF: 0.390

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		-0.049

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: rs10520722;

hg19: chr15-93905833;