chr15-93346230-C-G

Variant names:

• chr15-93346230-C-G
• rs17541406
• ENST00000543286.5:n.545+23884C>G

Variant summary

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

The ENST00000543286.5(ENSG00000257060):​n.545+23884C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 148,244 control chromosomes in the GnomAD database, including 10,230 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 0.35 (10230 hom., cov: 27)
• Consequence: ENSG00000257060 ENST00000543286.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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+23884C>G		intron	N/A
	ENSG00000257060	ENST00000553478.1	TSL:4	n.318+23884C>G		intron	N/A
	ENSG00000257060	ENST00000554105.6	TSL:4	n.422+23884C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.350 AC: 51885 AN: 148162 Hom.: 10229 Cov.: 27

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.442

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.350 AC: 51914 AN: 148244 Hom.: 10230 Cov.: 27 AF XY: 0.359 AC XY: 25779 AN XY: 71870

African (AFR) AF: 0.189 AC: 7619 AN: 40346

American (AMR) AF: 0.453 AC: 6690 AN: 14752

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3464

East Asian (EAS) AF: 0.628 AC: 3064 AN: 4878

South Asian (SAS) AF: 0.504 AC: 2371 AN: 4706

European-Finnish (FIN) AF: 0.448 AC: 4156 AN: 9268

Middle Eastern (MID) AF: 0.451 AC: 128 AN: 284

European-Non Finnish (NFE) AF: 0.378 AC: 25577 AN: 67606

Other (OTH) AF: 0.388 AC: 789 AN: 2034

Alfa AF: 0.236 Hom.: 626

Bravo AF: 0.347

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17541406; hg19: chr15-93889459;