rs12594966

Variant names:

• chr15-48027774-C-T
• rs12594966
• ENST00000560900.1:n.259-21016C>T

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.259-21016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 152,274 control chromosomes in the GnomAD database, including 336 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 0.021 (336 hom., cov: 33)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.319 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.259-21016C>T		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.252-21016C>T		intron	N/A
	ENSG00000259754	ENST00000665188.1		n.221-21063C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3268 AN: 152156 Hom.: 338 Cov.: 33

Gnomad AFR AF: 0.00645

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00654

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0214 AC: 3264 AN: 152274 Hom.: 336 Cov.: 33 AF XY: 0.0235 AC XY: 1750 AN XY: 74460

African (AFR) AF: 0.00643 AC: 267 AN: 41542

American (AMR) AF: 0.0299 AC: 457 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1718 AN: 5168

South Asian (SAS) AF: 0.0499 AC: 241 AN: 4830

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10618

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00654 AC: 445 AN: 68028

Other (OTH) AF: 0.0265 AC: 56 AN: 2110

Alfa AF: 0.00967 Hom.: 17

Bravo AF: 0.0230

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.81
PhyloP100		-1.1

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: rs12594966;

hg19: chr15-48319971;