15-47915269-C-T

Variant names:

• chr15-47915269-C-T
• rs549368
• ENST00000560900.1:n.195+30765C>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+30765C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 151,874 control chromosomes in the GnomAD database, including 2,081 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 0.16 (2081 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.175 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+30765C>T		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.189-77440C>T		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.189-77440C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24189 AN: 151752 Hom.: 2079 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.159 AC: 24203 AN: 151874 Hom.: 2081 Cov.: 31 AF XY: 0.160 AC XY: 11852 AN XY: 74224

African (AFR) AF: 0.117 AC: 4849 AN: 41490

American (AMR) AF: 0.163 AC: 2485 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3466

East Asian (EAS) AF: 0.163 AC: 814 AN: 4994

South Asian (SAS) AF: 0.181 AC: 870 AN: 4802

European-Finnish (FIN) AF: 0.157 AC: 1664 AN: 10574

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12070 AN: 67970

Other (OTH) AF: 0.186 AC: 392 AN: 2106

Alfa AF: 0.177 Hom.: 7308

Bravo AF: 0.160

Asia WGS AF: 0.182 AC: 629 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.67
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs549368; hg19: chr15-48207466;