15-99895823-T-C

Variant names:

• chr15-99895823-T-C
• rs1347479
• ENST00000660061.1:n.786-5573T>C

Variant summary

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

The ENST00000660061.1(ENSG00000259363):​n.786-5573T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,218 control chromosomes in the GnomAD database, including 3,025 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 0.19 (3025 hom., cov: 33)
• Consequence: ENSG00000259363 ENST00000660061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 1 publications found

Genes affected

ENSG00000259363 (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 (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660061.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259363	ENST00000660061.1		n.786-5573T>C		intron	N/A
	ENSG00000259363	ENST00000662069.1		n.785+18675T>C		intron	N/A
	ENSG00000259363	ENST00000668719.1		n.510-13260T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29073 AN: 152100 Hom.: 3015 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.191 AC: 29122 AN: 152218 Hom.: 3025 Cov.: 33 AF XY: 0.189 AC XY: 14080 AN XY: 74438

African (AFR) AF: 0.250 AC: 10389 AN: 41510

American (AMR) AF: 0.124 AC: 1892 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3470

East Asian (EAS) AF: 0.0503 AC: 261 AN: 5186

South Asian (SAS) AF: 0.109 AC: 526 AN: 4824

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10594

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12781 AN: 68010

Other (OTH) AF: 0.179 AC: 378 AN: 2112

Alfa AF: 0.186 Hom.: 6072

Bravo AF: 0.189

Asia WGS AF: 0.109 AC: 381 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	12
DANN	Benign	0.68
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs1347479; hg19: chr15-100436028;