15-47899501-C-T

Variant names:

• chr15-47899501-C-T
• rs479173
• ENST00000560900.1:n.195+14997C>T

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+14997C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,398 control chromosomes in the GnomAD database, including 6,089 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 0.21 (6089 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537
• Publications: 0 publications found

Genes affected

ENSG00000259754 (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 = 0.494 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. 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
	ENSG00000259754	ENST00000560900.1	TSL:4	n.195+14997C>T		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.188+86585C>T		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.188+86585C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31314 AN: 151292 Hom.: 6048 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0583

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0607

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.208 AC: 31416 AN: 151398 Hom.: 6089 Cov.: 31 AF XY: 0.208 AC XY: 15366 AN XY: 73962

African (AFR) AF: 0.499 AC: 20533 AN: 41128

American (AMR) AF: 0.171 AC: 2606 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0583 AC: 202 AN: 3466

East Asian (EAS) AF: 0.349 AC: 1784 AN: 5118

South Asian (SAS) AF: 0.204 AC: 978 AN: 4796

European-Finnish (FIN) AF: 0.0659 AC: 690 AN: 10464

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0607 AC: 4121 AN: 67910

Other (OTH) AF: 0.160 AC: 338 AN: 2110

Alfa AF: 0.0357 Hom.: 40

Bravo AF: 0.229

Asia WGS AF: 0.313 AC: 1086 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	7.5
DANN	Benign	0.35
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs479173; hg19: chr15-48191698;