rs12595668

Variant names:

• chr15-39281334-A-G
• rs12595668
• ENST00000558209.1:n.451+78455T>C

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+78455T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,102 control chromosomes in the GnomAD database, including 3,414 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 (3414 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 3 publications found

Genes affected

ENSG00000259345 (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 (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558209.1. 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
	ENSG00000259345	ENST00000558209.1	TSL:3	n.451+78455T>C		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.67+139575T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28456 AN: 151984 Hom.: 3410 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.187 AC: 28492 AN: 152102 Hom.: 3414 Cov.: 32 AF XY: 0.183 AC XY: 13595 AN XY: 74358

African (AFR) AF: 0.349 AC: 14453 AN: 41454

American (AMR) AF: 0.108 AC: 1644 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3468

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5184

South Asian (SAS) AF: 0.0940 AC: 453 AN: 4820

European-Finnish (FIN) AF: 0.158 AC: 1669 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9229 AN: 68004

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.147 Hom.: 2877

Bravo AF: 0.193

Asia WGS AF: 0.0550 AC: 191 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	0.84
DANN	Benign	0.71
PhyloP100		-0.55

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: rs12595668;

hg19: chr15-39573535;